https://doi.org/10.5281/zenodo.3688461
NEWS.md
# Revision history for the R/qtl package
## Version 1.74, 2025-12-08
- Removed includes of `R_ext/PrtUtil.h` which began causing warnings on CRAN.
## Version 1.72, 2025-11-19
### Minor changes
- Improve error message in cim() if multiple `pheno.col` provided,
as well as help file (to emphasize that only a single phenotype can
be considered.) (Issue #107)
## Version 1.70, 2024-08-21
### Minor changes
- Fixed a typo in the help file for `fitqtl()`.
- Small change to C code in simulate.c for R-devel: change calls to
Calloc, Realloc, and Free to R_Calloc, R_Realloc, and R_Free.
- In mqmdatatypes.cpp, changed calls to warning() to calls to Rf_warning()
to avoid compile error in R-devel.
- Add Authors@R field in the Description file
## Version 1.66, 2023-11-27
### Bug fixes
- Fixed problem in a call to Rprintf() in C++ code, identified by CRAN.
(Issue #104.)
- Fixed additional compiler warnings on CRAN (Issue #105).
## Version 1.62, 2023-11-17
### Bug fixes
- Fixed bug in `summary.scanone()` for the case `format="onepheno"` but
`threshold` has length > 1. (Issue #102.)
- Fixed bug in `read.cross()` for format `"csvs"` when the phenotype
file contains only the identifiers. (Issue #103.)
## Version 1.60, 2023-04-18
### Minor changes
- In the CITATION file, change from `citEntry()` to `bibentry()`.
### Bug fixes
- Fixed bug in addint() and addcovarint(): when X chr QTL and missing
phenotypes, would halt with error because cross wasn't getting
subset. (Issue #101)
## Version 1.58, 2022-12-22
### Minor changes
- In compiled code, replace calls to `sprintf()` with calls to
`snprintf()`, to avoid warnings on CRAN.
## Version 1.54, 2022-12-01
### Minor changes
- `locateXO()` and `countXO()` are now working for cross type BCsFt
(by treating it as an F2 intercross).
### Bug fixes
- Fixed a bug in `summary.cross()` re `&` vs `&&`.
- Fix bug in `read.cross.bcsft()` so that in `read.cross()` you can
use `crosstype="bcsft"`
## Version 1.52, 2022-07-09
### Minor changes
- `checkAlleles()` checks that the recombination fractions in the
cross object are not only LOD scores (such as from `markerlrt()`);
if they are, it re-runs `est.rf()`.
- In `sim.ril()`, changed an instance of `if(class(x)=="X")` to
`if(inherits(x, "X"))`
## Version 1.50, 2021-10-06
### New features
- `cim()` now includes an `addcovar` argument for including additional
covariates in the model.
### Minor changes
- Revised qtlversion() to handle a case like "1.50".
- Added `#define USE_FC_LEN_T` in C code that calls Fortran, because
of a change in R 3.6.5 that's going to be required in R 4.2.0.
## Version 1.48, 2021-03-24
### Bug fixes
- Fixed bug in `addqtl()` and `addpair()` in which the argument
`forceXcovar` wasn't getting passed to `scanqtl()`.
- Fixed bug in `stepwiseqtl()` regarding the way the null LOD score is
calculated.
## Version 1.47, 2021-01-07
### Minor changes
- Added function `find_large_intervals()` for finding inter-marker
intervals in a map with length greater than some value.
- Fixed potential problem in documentation, since `plot()` has moved
from the graphics package to base.
- Acknowledge R Core Team among contributors, as zeroin function
(in C) had been taken from R version 2.15.1. Also add a Copyrights
field to the DESCRIPTION file.
- Allow `rescalemap()`, `shiftmap()`, `summaryMap()`, and
`jittermap()` to work with plain lists.
- Fixed Issue #91 where pull.rf() gives a cryptic error if marker
names are not all distinct.
### Bug fixes
- Fix a problem in `inferredpartitions()` that occurs in the devel
version of R.
- Small change to `read.cross()` to avoid warning about length of
`alleles` argument for `crosstype="4way"`. (Fixes Issue #90.)
- Small change to `read.cross()` to avoid messing with X chromosome
genotypes when `crosstype=4way"`. (Fixes Issue #88.)
## Version 1.46, 2020-02-28
### Minor changes
- In preparation for R 4.0, when the default for `stringsAsFactors`
will become `FALSE` rather than `TRUE` in `read.table()` and
`data.frame()`, we needed to add `stringsAsFactors=TRUE` to calls to
`read.table()` and `data.frame()` in various places. Also there was
some ugliness regarding `addpair()`.
### Bug fixes
- Fix bug in `mqmpermutation()` by removing the uses of batches and
the `batchsize` argument.
## Version 1.45, 2020-02-01
### Minor changes
- Added `plot()` and `summary()` functions for the output of
`comparegeno()`.
- Added internal functions `crosstype()` and `chrtype()`.
- Added argument `crosstype` to internal function `fitqtlengine()`
rather than taking it from the cross attributes.
- Went through full package to replace use of `class(blah)=="blah"`
with `inherits(blah, "blah")`.
- mqmscan() and mqmscanall() now give a warning about omitting the X
chromosome, and give a more meaningful error if there are no autosomes.
- Improved warning and error messages in several places: rather than
"Chromosome misspecified" say "Chromosome __ not found"
### Bug fixes
- Fix bug regarding missing phenotypes in `stepwiseqtl()`.
- Fix bug in `addpair()` re converting map to data frame (getting
error like `cannot coerce class "A" to data.frame`).
- Fix bug related to reading 4-way cross data, to ensure that the
genetic map for each chromosome is a 2-row matrix.
- Fix bug in `refineqtl()` that gave a warning about `min(diff(a))`
when there was a single marker on a chromosome.
([Issue #78](https://github.com/kbroman/qtl/issues/78))
- Added explanations of a couple of arguments for mqmscan() that had
previously not been explained.
## Version 1.44, 2019-01-22
### Minor changes
- Added col argument to geno.image() for custom colors.
- Revision to plot.scanone() to handle +/- Inf in the LOD score column.
- Add better error message in read.cross with format="mapqtl"
- Revision to summary.map to just give warning if input does not have
class "cross" or "map".
- Improved error message in scanone() when phenotypes are not numeric.
- Small change in getgenonames() to avoid a problem if there aren't
enough allele codes.
- plotLodProfile() now gives a more informative error message if
called with a null QTL model.
- Revised mqmplot.circle() so that chromosome IDs don't need to be
numbers.
- Fix small bugs in c.cross() and checkcovar().
## Version 1.42, 2018-02-19
### Major changes:
- Removed the functions plot.errorlod, plot.geno, plot.info,
plot.missing, plot.pheno, plot.pxg, and plot.rf. Changes in the
process of submitting packages to CRAN have made this necessary.
Each of the packages has alternative names that have been used in
the tutorials for some years:
```
plot.errorlod plotErrorlod
plot.geno plotGeno
plot.info plotInfo
plot.missing plotMissing
plot.pheno plotPheno
plot.pxg plotPXG
plot.rf plotRF
```
If you have old scripts that use these function names, add the
following code at the top:
```
source("https://rqtl.org/dotfunc.R")
```
### Minor changes:
- Fixed a bug in stepwiseqtl() regarding model="binary"; a number of
cases where I wasn't passing model to other functions, like
refineqtl().
- Dealt with possibility NA LOD scores in refineqtl().
- Removed questionable use of try() from subset.scanoneperm() and
subset.scantwoperm().
- Fixed a bug in mqmscanfdr (to permute all chromosomes not just
chromosome 1).
- Made estimate.map=FALSE the default in read.cross.
- Revised read.cross for the "bcsft" cross type so that it should be
able to handle sep=";".
- Removed the file vignettes/fancyheadings.sty
- Fixed a couple of minor problems that showed up in byte-compiling
the package (breaks outside of loops and use of <<-)
## Version 1.41, 2017-06-11
### Major changes:
- None.
### Minor changes:
- Fixed bugs in formMarkerCovar to give better error messages if
markers aren't found.
- Fixed a bug in reviseXdata in case of intercross with both sexes but
backward direction only.
- Fixed a bug in mqmscan that gave an error about duplicate row names.
- Fixed a bug in summary.scantwo for the case of autosome/X chromosome
specific permutations.
- Fix bugs in pull.argmaxgeno and pull.genoprob for 4-way crosses with
include.pos.info=TRUE. (Need to account for map being a matrix.)
## Version 1.40, 2016-10-31
### Major changes:
- cim() now halts with an error for cross type "4way". The method has
not been implemented for 4-way crosses, and the results are not
meaningful.
### Minor changes:
- Small change to the way Bayesian credible intervals are calculated
by bayesint(), concerning the treatment of widths of intervals
between positions.
- Fix bug in switchAlleles() so that it works with cross type "bcsft"
(and will give an appropriate error message for unsupported cross
types).
- sim.cross gives a warning if model is specified but not used (this
is the case for RILs, where we've not implemented the simulation of
QTL effects)
- plot.pxg (aka plotPXG) passes ... to plot(), so now you can control
the y-axis limits via ylim.
- Fixed a problem with column names of output of scantwopermhk.
## Version 1.39, 2016-03-04
### Major changes:
- Fixed a bug in scantwo() when using weights with multiple phenotypes
when some of the phenotypes contain missing values. (This is the
same as the bug fix in scanone in version 1.38. Reminder of
important principle: when you find a bug, look for other possible
instances of the same bug.)
- Changed the color scheme for plot.scantwo and plot.rf from red/blue
rainbow to Viridis (see Option D at https://bids.github.io/colormap/)
The plot.rf function has a new argument col.scheme; if you want to
use the old red/blue scheme, use col.scheme="redblue".
- Fixed a bug in cim() that was causing a segmentation fault.
### Minor changes:
- Added a function table2map() for converting a data frame with marker
positions (chr, position) into a map object.
- Added a bit more detail in the help file for readMWril().
## Version 1.38, 2015-12-03
### Major changes:
- Get rid of everything to do with degrees of freedom in scanone and
scantwo. The checks seem to offer little value but rather produce
cryptic warnings that confuse many users.
- Fixed a bug in scanone() when using weights with multiple phenotypes
when some of the phenotypes contain missing values.
### Minor changes:
- In plotLodProfile, if col has length > 1 but no equal to the number
of QTL, give a warning, but either repeat or subset the vector
rather than just using the first value.
- Modified read.cross with format "mm" to handle files with "bc" where
we usually see "backcross".
## Version 1.37, 2015-08-24
### Major changes:
- None.
### Minor changes:
- In read.cross with format="csv", "mm", or "tidy", don't let it
reorder the chromosomes (which it would do if there were chromosomes
named other than numbers < 1000, "X", or "x").
- drop.markers now gives an error if you try to drop *all* of the
markers.
- If cross object contains no genotype data, totmar() and nmar() now
give more meaningful errors.
- Fixed a bug in scantwo and scantwopermhk in which an error would
occur if reduce2grid had been called and assumeCondIndep=FALSE. Now
forcing assumeCondIndep=TRUE in this case.
- Fixed a bug in plot.pxg, in the case that not all possible genotypes
were observed at a marker.
- Fixed a bug in stepwiseqtl, where if covar is not a data frame, they
don't get considered in the model.
- Fixed a bug in fill.geno for method="maxmarginal" (wasn't putting NAs in
genotypes with probability < min.prob)
- Fixed a bug in refineqtl that arises when multiple QTL are at exactly
the same position, which can arise in stepwiseqtl.
## Version 1.36, 2015-03-05
### Major changes:
- None.
### Minor changes:
- Added a function flip.order() for flipping the order of markers on
selected chromosomes.
- Added scanonevar.meanperm and scanonevar.varperm (from Robert Corty)
for permutation tests with scanonevar().
- Revised plotPheno (aka plot.pheno) so that one can control the
x-axis label and title (also, in a histogram, the breaks).
- plotPXG: if infer=FALSE and there are no fully-informative genotypes
(e.g., in a 4-way cross), give a more informative error.
- geno.image: allow control of x- and y-axis labels; allow suppression
of axes.
- Removed some warnings about missing end-of-line characters, in
read.cross with MapQTL format.
- Fixed a bug in scanonevar; was failing with an error about coercing
class "A" to a data.frame
- Dropped the name summary.scantwo.old(); still available as
summaryScantwoOld().
## Version 1.35, 2014-12-15:
### Major changes:
- None.
### Minor changes:
- Fix an important bug in summary.cross.
- Change a couple of abs() to fabs() in C code.
## Version 1.34, 2014-10-30:
### Major changes:
- Added ability to do X-chr-specific permutations in scantwo (argument
perm.Xsp, as in scanone). Separate thresholds are obtained for the
regions A:A, A:X, and X:X regions, maintaining control of the
overall false positive rates.
- Added a function scantwopermhk that just performs scantwo
permutations with Haley-Knott regression; faster and with lower
memory usage than scantwo.
- With X-chr-specific scantwo permutations, calc.penalties will give
separate main effect for autosome and X chromosome, and separate
interaction penalties for A:A, A:X, X:X. For A:A interactions, we
still use "light" and "heavy" penalties; for A:X and X:X
interactions, only the "heavy" penalty is used. These penalties may
be used in stepwiseqtl for better treatment of the X chromosome in
automated inference of multi-QTL models.
- Added scanonevar() function, for a single-QTL genome scan for QTL
affecting not just the mean phenotype but also the variance. (Code
from Lars Ronnegard; method in Ronnegard and Valdar Genetics
188:435-447, 2011.)
- Added "tidy" format to read.cross and write.cross. This separates
the data into three comma-delimited files, for genotypes,
phenotypes, and the marker map. Separating the data in this way
allows each file to be in a simpler format.
### Minor changes:
- Add another option to fill.geno: impute using maximum marginal
probability.
- Add function map2table (output like pull.map with as.table=TRUE, but
starting with a map rather than with a cross).
- Fixed a bug in est_map_ri8self.c (thanks to Rohan Shah)
- Fixed a bug in scanone/scantwo stratified permutations in batch,
with multiple phenotypes, some with missing values (thanks to
John Lovell).
- Fixed some bugs in read.cross with format="mapqtl".
## Version 1.33, 2014-08-12:
### Major changes:
- Can read/write 4-way cross data in MapQTL format (thanks to Timothee
Flutre).
### Minor changes:
- read.cross with format="qtlcart" can now read doubled haploids
(dh/Ri0).
- Fixed potential problem in read.cross with format="csv" or "csvs" when
there are many empty cells in the phenotype data.
- Fixed bug in read.cross for format="csv" that shows up in some rare
cases: markers not ordered by linkage group, no positions provided,
and chromosome IDs non-numeric. It was a pretty bad bug, as marker
genotypes got scrambled.
- Fixed some memory leaks in MQM code.
## Version 1.32, 2014-05-28:
### Major changes:
- None.
### Minor changes:
- fitqtl with model="normal" now returns residuals as an attribute.
- Added an additional argument to plot.scanone, bgrect, for making the
background of the plotting region a different color.
- Revised cleanGeno to work with any cross having two possible
genotypes (i.e., not just bc but also riself, risib, dh, haploid).
- Revised summary.cross so that overall genotype frequencies are given
separately for autosomes and the X chromosome.
- Fixed typo in a warning in add.threshold.
- Fixed a bug in reduce2grid, regarding format of attributes
- Fixed a bug in MQM: in some circumstances, the last marker was
always included as cofactor; other cleanup in MQM code.
## Version 1.31, 3/19/2014:
### Major changes:
- Added a function reduce2grid() for subsetting the genotype
probabilities (from calc.genoprob) or imputations (from sim.geno) to
the evenly spaced grid of pseudomarkers, for use in the case of very
dense markers when it is too computationally intensive to perform a
genome scan at both the markers and the grid of pseudomarkers.
### Minor changes:
- Fixed a problem in write.cross with format="csv" (for cross types
other than BC and F2, it would use incorrect genotype codes if there
was no "allele" attribute for the cross).
- Add a couple of arguments to plotLodProfile: showallchr, to show all
chromosomes (and not just those with QTL), and textsep, to control
the separation between the QTL labels and the LOD curves.
- Fix a bug in bcsft.c, regarding potentially over-running an array
- Fix problem with plotLodProfile when it's maximized at multiple
locations.
- Fix problem in refineqtl and stepwiseqtl; map attribute in qtl
object would get unintentionally subsetted if the qtl object needed
to be re-created.
- In addqtl, addint, and addcovarint, have require.fullrank=FALSE be
the default; require.fullrank=TRUE remains the default in
stepwiseqtl.
- Fixed bug in which summary.scantwo was re-ordering the chromosome
factor levels.
## Version 1.30, 2/10/2014:
### Major changes:
- Revised parallel code (in scanone, scantwo, mqmpermutation, and
mqmscanall) to use a different function for Windows, as mclapply()
doesn't work there.
### Minor changes:
- Fixed problem in formLinkageGroups when used with results of
markerlrt(): no recombination fractions so use max.rf=Inf
- Added arguments type, cex, pch, and bg to plot.scanone, to be passed
to lines() in making the plot. Thus, you can use type="p" to get
points only.
- Fixed a bug in scanqtl that showed up if there were missing
phenotypes and no covariates.
## Version 1.29, 12/9/2013:
### Major changes:
- None.
### Minor changes:
- Slight change to summary.qtl to deal with QTL objects with no QTL.
- For the QTLRel package, now "export" reviseXdata() in NAMESPACE.
## Version 1.28, 9/23/2013:
### Major changes:
- Added cross type "haploid". Like backcross ("bc") or doubled
haploids ("dh") but with genotype labels like "A" and "B" instead of
"AA" and "AB"/"BB".
- Added crosstype argument to read.cross, to force a particular cross
type (such as "riself").
- For parallel processing, replaced reliance on the snow library with
the use of the parallel library.
### Minor changes:
- Added formMarkerCovar(), to facilitate use of markers as covariates
in QTL analysis.
- Added function addmarker() for adding genotypes for a marker to a
cross object.
- Added function nqtl() for counting number of QTL in QTL object.
- Added examples to help files for plotPXG and effectplot on getting the
output.
- Slight change to way to handle random number generation for
cluster-based computing.
- Fix bug in fitqtl-link functions for model="binary" (re matrix rank)
- Fixed write.cross to allow use for BCsFt crosses.
- Fixed an out-of-bounds error in the C++ code mqmscan.cpp.
- In stepwiseqtl with verbose=FALSE, the initial LOD score is no
longer printed.
## Version 1.27, 4/11/2013:
### Major changes:
- Implemented HMM algorithms for advanced backcross/intercross.
### Minor changes:
- Improvement in addqtl, addint, scanqtl, stepwiseqtl
to better handle collinearity in the design matrix that could give
spurious evidence for QTL in large QTL models. This can still be a
problem with addpair (and stepwiseqtl with scan.pairs=TRUE).
- Slight change to help file for read.cross, to be more explicit about
the "csvs" format.
- Fixed a bug in read.cross for format="qtlcart" with RIL data.
- Made cross type in "qtlcart" files case insensitive in read.cross.
For example, any of Ri1, RI1, rI1, or ri1 will be treated the same.
## Version 1.26, 11/27/2012:
### Major changes:
- We changed the treatment of the ind argument in subset.cross to
avoid problems that occurred when the cross contained numeric
individual IDs. Now, we match the values in ind against the
individual IDs only if ind values are character strings. If the ind
values are numeric, we treat them as numeric indices and they are
not compared against the individual IDs.
### Minor changes:
- In plot.rfmatrix, include marker name in title (unless main is
provided as an argument).
- Add warning message to find.marker if there's no match for a given
chromosome name.
- Slight change in find.markerpos(), to speed it up.
- Slight change to locateXO to save genotypes to left and right of
each crossover.
- Small addition to the "A shorter tutorial of R/qtl" (rqtltour2.pdf).
- Fixed slight bug in summary.scanone for format="tabByChr" or
format="tabByCol".
- Fixed bug in fitqtl for case that individuals have missing
phenotypes or covariates and there's a QTL on the X chromosome
- Fixed bug in effectplot, regarding coding of genotypes on the X
chromosome.
- Fixed bug in mqmscan for case when estimate.map=TRUE but plot=FALSE.
- Fixed bug in c.cross for case that there are different sets of markers.
- Fixed bug in xaxisloc.scanone for case that chromosomes don't start at 0.
- Fixed bug in locateXO; gave core dump if there was just one marker on
the chromosome.
- Fixed bug in scanone and scantwo for case that weights are used but
there are individuals with missing phenotype; the weights weren't
being subsetted appropriately.
- Revised example help file for multitrait data to use mqmscanall
rather than scanall, since the latter function has no help file.
- scanPhyloQTL now gives warning if there are different marker maps.
- Fixed bug in mqmaugment; with one phenotype, its name was getting
changed to "pheno".
## Version 1.25, 8/13/2012:
### Major changes:
- None.
### Minor changes:
- Revised write.cross to output data in "qtab" format; see
https://github.com/qtlHD/qtlHD/blob/master/doc/input/qtab.md
- Revised summary.scanone to be more consistent about only picking one
row per chromosome even when there are multiple positions sharing
the maximum LOD on that chromosome.
- Fixed bug in stepwiseqtl; backward deletion steps were not dealing
with the drop-one-qtl results from fitqtl appropriately.
- Revised fitqtl to include formulas and lod scores as attribute in
drop-one-qtl analysis.
- Fixed a bug in fitqtl regarding the adjustment for the X
chromosome. The problem shows up in stepwiseqtl; if X chr enters
model and is then removed, the covariates adjusting for sex and pgm
continue to be used. Added argument to refineqtl, fitqtl, scanqtl,
addqtl, addpair, to force X-related covariates into model.
- In stepwiseqtl, include penalties as attribute in the output.
- Slight change to checkcovar(): omit individuals with
phenotypes/covariates that are +/- Inf, as well as those that are
missing.
- Handle missing values in mf.stahl and imf.stahl.
- Fixed rare bug in fitqtl regarding X chr loci with interactions.
- Fixed bug in sim.cross for type="bc" that resulted in loss of "X"
chromosome type.
- Speed up some of the examples in the help file, so that R CMD check
doesn't take so long.
## Version 1.24, 5/25/2012:
### Major changes:
- Fixed a major bug in checkcovar, used by scanone and scantwo to omit
individuals with missing phenotypes. If there is an "ID" column
that is numeric, the wrong individuals could be omitted, and
genotypes and phenotypes would be misaligned.
- Changed the names of a number of functions, in order to avoid the
"Note" in R CMD check, and because Prof. Brian Ripley asked me to.
```
plot.map -> plotMap
plot.missing -> plotMissing
plot.errorlod -> plotErrorlod
plot.geno -> plotGeno
plot.info -> plotInfo
plot.pheno -> plotPheno
plot.pxg -> plotPXG
plot.rf -> plotRF
summary.map -> summaryMap
summary.scantwo.old -> summaryScantwoOld
```
- Revised tutorials to use the new naming scheme.
- Revised the emission probabilities for dominant markers in an F2,
for the HMM calculations. Previously, we had
Pr(O = not A | g = AA) = Pr(O = not B | g = BB) = epsilon/2
these have been changed to
Pr(O = not A | g = AA) = Pr(O = not B | g = BB) = epsilon
This corresponds to "not A" being "H or B"; similarly for not B.
Results will change only for an intercross with dominant markers,
and generally only slightly.
### Minor changes:
- Changes to the format of the output of summary.scanPhyloQTL for
format="lod". The final column is now the maximum LOD score across
partitions; the difference between the maximum and the
second-highest is now third-to-last; the threshold argument is
applied to the overall maximum rather than to that difference.
- Revisions to read.cross (for the csv formats) from Steffen Moeller,
to give some more informative warnings/errors.
- Fixed a bug in scantwo permutations in case that a chromosome has
multiple markers but they span < step from calc.genoprob.
- Fixed a bug in interpPositions; problems if the input had missing
rownames.
- Renamed the README.txt file as INSTALL_ME.txt; added a new
README.txt that provides a brief description of the package.
## Version 1.23, 3/6/2012:
### Major changes:
- None.
### Minor changes:
- Added functions pull.genoprob, pull.argmaxgeno, and pull.draws, to
pull out those bits from a cross object as a single big matrix or
array.
- Added a function inferFounderHap() for crudely inferring founder
haplotypes in multi-parent RIL, using groups of adjacent markers.
- Added function nullmarkers() for identifying markers with no
genotype data.
- Revised sim.cross so that founder genotypes are included in output,
for 4- and 8-way RIL.
- Added HMM functions to handle a special design for MAGIC lines from
BioGemma (http://www.biogemma.fr/indexuk.php).
- Revised subset.cross and clean.cross so that cross information in 4-
and 8-way RIL don't get lost.
- Revised plot.pxg, effectplot and effectscan to give a more
informative error if the selected phenotype is not numeric.
- Revised qtlversion() to use packageVersion().
- Fixed bug in summary.map: class included the function data.frame;
not just the character string "data.frame".
- Revised various utility functions to retain the "onlylod" attribute
in cross$rf, if it's there.
## Version 1.22, 11/28/2011:
### Major changes:
- Revised plot.map to deal with a pair of maps with markers in
different orders (or with some markers appearing in one map and not
the other). We still require that the two maps have the same
chromosomes and chromosome names (with chromosomes in the same
order).
- Revised scantwo to allow analysis of individual chromosome pairs,
and reorganized the way that scantwo permutations are done (first
summarizing each chromosome pair and then overall); this should
eliminate the memory problems we've had with scantwo permutations.
### Minor changes:
- Added warning to help file for fitqtl() regarding the estimated
percent variance explained in the case of linked loci: the values
are misleading.
- Fixed problem in comparecrosses() regarding Inf/-Inf phenotypes.
- Fixed a bug in scantwo, method="hk", for multiple phenotypes or
permutation tests in batch. This showed up only when there were
missing genotypes at one or both putative QTL.
- write.cross with format="csv" now exports genotypes as AA/BB for
RIL (previously, genotypes were written as AA/AB).
- Fixed bug in addint() and addcovarint()
- Revised typingGap to have an argument 'terminal'; if TRUE, just look
at the gap from the terminal markers to the first typed interior
marker, giving 0 if the terminal markers are both typed.
- Fixed bug in calc.genoprob with stepwidth="max" in the case that no
pseudomarkers are to be added.
- Fixed bug in geno.table for the case that X chromosome has just one
observed genotype.
- No longer allow "" in na.strings in read.cross for csv files.
- Revised all calls to data.frame() and as.data.frame() to override
global option of stringsAsFactors, so that we know what's going to
happen.
- Revised scantwo so that if the 'chr' argument is a list, we do just
the scans of the chr in the first component against those in the
second component.
- Slight change in plot.info to deal with inclusion of 'main'
argument.
- Added NAMESPACE file.
- Slight changes to avoid some R warning messages.
- Slight change to imf.cf to give more accurate results.
- Fixed warning message in replacemap.
- Fixed warning message in +.scanone.
- Fixed bug in mqmfind.marker.
- Fixed slight bugs in print.addint and print.addcovarint.
- Removed a bunch of unused variables from C code.
## Version 1.21, 3/21/2011:
### Major changes:
- None.
### Minor changes:
- Add "addchr" argument to find.pseudomarker. The default is TRUE,
and returned non-marker locations have names like "c5.loc25" (as in
the output of scanone). If FALSE, that initial "c5." part is left
off, to return just strings like "loc25" (as in the genotype
probabilities from calc.genoprob).
- Revise calls to rainbow() in plot.rf and plot.scantwo so that they
no longer use the 'gamma' argument, which is being removed from
future versions of R.
- Slight change to format of verbose output in est.map with m>0 (that
is, under interference).
## Version 1.20, 2/18/2011:
### Major changes:
- Enabled est.map to use multiple processors via snow; added argument
n.cluster to indicate the number of cluster nodes to use.
- Added the option stepwidth="max" in calc.genoprob, sim.geno, and
argmax.geno. This inserts the minimal number of pseudomarkers so
that the maximum step between points is as indicated by the "step"
argument.
### Minor changes:
- Fixed a bug in refineqtl() that kept it from working for a 4-way
cross. (The bug also broke stepwiseqtl().)
- Fixed a problem in the internal function dropXcol() that led to a
crash in scantwo() for 4-way crosses with an X chromosome.
- Fixed a bug in mqmscan() regarding the chromosome names in the
output.
- Trap cases of X chromosome for crosses other than bc/f2 in
stepwiseqtl, makeqtl, addqtl, and addpair.
- Added a function phenames() for pulling out the names of the
phenotypes.
- Small revisions and enhancements to some of the MQM plots.
- Revised subset.cross so that if the cross contains QTL genotypes
(from sim.cross), these are also subsetted.
- Revised replacemap.cross (aka replace.map) so that it will also
replace the maps in results from calc.genoprob, sim.geno and
argmax.geno, using interpolation if necessary.
- Fixed a couple of minor bugs in mqmscan: one giving duplicate row
names, another resulting in pseudomarkers outside the terminal
markers even when off.end=0.
- Fixed bugs in scanone and scantwo regarding batch mode for
model != "normal".
- Fixed a bug in refineqtl; it was including all possible covariates
refered to in the data frame 'covar', even if they weren't referred
to in the formula.
- Fixed a bug in plot.geno, introduced in version 1.19, that made it
not work with horizontal=FALSE.
## Version 1.19, 11/29/2010:
### Major changes:
- Added a tutorial on genetic map construction; find it within the
package at docs/geneticmaps.pdf, or (more simply, probably), find it
on the web at https://rqtl.org/tutorials/geneticmaps.pdf
- Added two additional formats to summary.scanone(), "tabByCol" and
"tabByChr". These produce tables of LOD peaks organized by LOD
score column or by chromosome. The tables include approximate
confidence intervals for QTL location (as calculated by the lodint()
or bayesint() function; which one is indicated by the new argument
ci.function). Here's an example:
```
bp:
chr pos ci.low ci.high lod pval
c1.loc44.5 1 47.8 35.5 85.0 3.56 0.007
D4Mit164 4 29.5 18.8 30.6 8.09 0.000
sqrt:
chr pos ci.low ci.high lod pval
c1.loc44.5 1 47.8 35.5 84.8 3.63 0.007
D4Mit164 4 29.5 17.2 30.6 8.08 0.000
```
### Minor changes:
- Revised summary.scanoneperm to include a new argument,
controlAcrossCol. If TRUE, LOD thresholds will control error rate
not just across the genome but also across the LOD score columns.
- Added function droponemarker, with the aim of identifying
problematic markers by dropping one marker at a time and calculating
a LOD score and a change in the estimated genetic length of the
respective chromosome.
- Added a function pull.rf for pulling out either the estimated
recombination fractions or the lod scores, as calculated by
est.rf(), from a cross object. Also added a function plot.rfmatrix,
for plotting a slice through these.
- Added a function cleanGeno for removing genotypes that are possibly
in error (as indicated by apparent tight double-crossovers). Use
this function with caution.
- Added a function typingGap, which calculates, for each individual
and each chromosome, the maximum distance between typed markers.
- Revised MQMscan so that the output contains covariate information,
to be plotted with add.cim.covar().
- Revised c.scanone(), c.scanoneperm, c.scantwo, and c.scantwoperm so
that the input "..." can be a list of
scanone/scanoneperm/scantwo/scantwoperm objects.
- Revised plot.geno() so that, for the X chromosome in a backcross or
intercross, the genotypes appear appropriately, with females being
homozygous or heterozygous and the males hemizygous, though we plot
the hemizygous genotypes as if they were homozygotes.
- Revised subset.scanoneperm and subset.scantwoperm so that one may
pull out a subset of replicates (not just columns). Added functions
[.scanoneperm and [.scantwoperm so that one can use [] to subset.
- Revised locateXO() so that the output contains a column with the
number of typed markers between adjacent crossovers.
- In orderMarkers(), if verbose is numeric and > 1, even more
information on the progress of the calculations is provided.
- Fixed a problem in subset.cross where, in the case that a cross
contained numeric IDs, subsetting the individuals resulted in them
being sorted according to their IDs.
- Added a manual page for the function getid(), which was not previously
documented. (It is used internally a great deal, and it may be
useful more generally.)
- Revised effectplot so that if mname2 or mark2 are given but mname1
and mark1 are not, the arguments get switched.
- Fixed a bug in shiftmap().
- Added an argument, force, to reviseXdata(), to force a change in the
genotypes; this is for use within plot.geno().
- Slight change to top.errorlod, so that the output columns are not
factors but character strings.
- Slight change in plot.geno() so that we use filled circles (pch=23) rather
than calling points() twice for each point.
- Small changes to mqmplot.circle().
- Subtle changes to tutorials new_multiqtl.pdf,
new_summary_scanone.pdf, new_summary_scantwo.pdf; added .R files
with the code for these tutorials.
- Fixed slight bug in getid().
## Version 1.18, 8/18/2010:
### Major changes:
- None.
### Minor changes:
- Revised geno.table so that, for 4-way crosses, it gives P-values in
most cases. (Previously, it just did so for fully informative
markers.)
- Changed the default format for max.scanPhyloQTL and
summary.scanPhyloQTL from format="lod" to format="postprob".
- Added function inferredpartitions for pulling out the inferred
partitions for a specified chromosome from the output of
scanPhyloQTL.
- Fixed a problem in ripple with method="likelihood". (The problem
arose in revisions in version 1.17.)
- Fixed a problem in est.map that resulted in NAs. (The problem arose
in revisions in version 1.17.)
- Slight changes to "inverse" map functions imf.k, imf.h, imf.cf, so
that recombination fractions >= 0.5 return large map distances
rather than NAs.
- Fixed a bug in summary.scanPhyloQTL so that it works when the input
has just one chromosome and so the colnames remain like "AB|CD"
rather than getting converted to "AB.CD".
## Version 1.17, 7/28/2010:
### Major changes:
- Implemented the fit of models for binary traits in fitqtl(), by
Haley-Knott regression and multiple imputation. This model can also
be used in refineqtl, scanqtl, addqtl, addpair, addint, stepwiseqtl,
and addcovarint.
- Implemented Haley-Knott regression for binary traits in scanone and
scantwo.
- In mqmscan(), replaced the arguments step.min and step.max with
a single argument, off.end (to be more like scanone).
- Added functions for the joint analysis of multiple crosses, in order
to map QTL to a phylogenetic tree. (A paper describing the methods
is in preparation.) The key function is scanPhyloQTL. simPhyloQTL
is used to simulate data. plot.scanPhyloQTL, max.scanPhyloQTL, and
summary.scanPhyloQTL are the plot, max, and summary functions for
the output from scanPhyloQTL.
### Minor changes:
- Added 'offset' argument to est.map, which defines the starting position
for each chromosome. If missing, we use the starting positions that
are currently present in the input cross object.
- Added function shiftmap, for shifting the starting points of a
genetic map (in a map or cross object).
- Added function switchAlleles, for switching the alleles at selected
markers in a cross object. (For example, in a backcross, switching
AA and AB at a marker; in an intercross, exchanging AA for BB.)
- Revised geno.table to have an additional argument, scanone.output.
If scanone.output=TRUE, the output is as produced by scanone(), so
that one may use plot.scanone() to plot the results.
- Added the ability to have ripple() run in parallel, if the snow
package is installed. The added argument n.cluster indicates the
number of parallel nodes to use. This is reapply only useful with
method="likelihood"; with method="countxo", it can be slower than
just using one CPU.
- Added a function pull.markers, which is the opposite of
drop.markers.
- Added a function drop.dupmarkers, for dropping markers with
duplicate names.
- Added an argument 'bandcol' in plot.scanone, to specify a color for
alternating bands to indicate chromosomes. The default
(bandcol=NULL) is to not plot such bands. A good choice might be
bandcol="gray70".
- Added an argument 'chr' in est.map, to estimate maps for just a
subset of chromosomes.
- Revised replace.map (and replacemap.cross) so that the map can have
just a subset of the chromosomes in the cross, in which case only
the maps for that subset are replaced.
- Changed the default in plot.info from method="both" to
method="entropy". Also, added an argument "fourwaycross", so that
one can look at the missing information just for the alleles of the
first parent (A vs B) or the second parent (C vs D). Finally, added
an argument "include.genofreq"; if TRUE, the results will include
estimated genotype frequencies at each position.
- Added argument 'simple' to summary.fitqtl, addint, and addcovarint;
if TRUE, output includes neither p-values nor sums of squares.
- Added a function allchrsplits(), for testing whether to split a
linkage group/chromosome into two, by calculating a LOD score for
each interval comparing the full linkage group to the split into two
groups at that interval.
- Added a function nqrank() for transforming a numeric vector into the
corresponding normal quantiles.
- Fixed a problem in MQM code regarding negative or really large
marker positions.
- Fixed a bug in mqmpermutation(), where it was using the wrong
phenotype name in the output, if pheno.col is something other than
1.
- Revised est.map for 4-way crosses slightly. We'd previously
randomized the map before starting EM, which seemed a bad idea.
- Fixed a bug in scantwo() for the case that multiple phenotype
columns are considered but they have different patterns of missing
data. An error occurred due to a number of stupid small mistakes.
[Thanks to Ricardo Verdugo for reporting the problem.]
- Revised summary.cross so that if markers are at the same location,
the warning message indicates which chromosomes are involved.
- Revised summary.scanone so that if there is one LOD score column in
the output, but the permutation results have more than one, then
the first column in the permutation results is used and the others
are ignored (and a warning, rather than an error, is issued).
- Revised calc.plod() to allow penalties to be infinite.
- Revised read.cross with format="csv" to give an error if the 2nd row
has all blanks.
- Revised plot.scanoneboot, plot.scanoneperm, and plot.scantwoperm so
that they can use the ... argument more flexibly. [I use a scheme
suggested by Brian Yandell.]
- Revised plot.geno so that the ... argument can include xlim and
ylim.
- Fixed bug in convert2sa for case of chromosome with just 1 or 2
markers.
- Fixed bug in refineqtl that resulted in sometimes the rownames in
the lod profile attribute being messed up.
- Revised scanone and scantwo to trap error if perm.strata is not of
the correct length.
- Added argument 'ind.noqtl' to scanone, which indicates individuals
that are assigned no QTL effect. This is for rare (largely
internal) use for the case that one is combining multiple crosses.
- Fix bug in internal function create.map, for case of a sex-specific
map with very small length.
## Version 1.16, 5/23/2010:
### Major changes:
- None.
### Minor changes:
- Revised fitqtl() so that estimated QTL effects in RIL or doubled
haploid are as they should be (half the difference between the two
homoyzogotes).
- Added a function rescalemap for rescaling a genetic map (as for the
case that a cross object has marker positions in basepairs and one
wishes to convert them to Mbp or some approximation of cM
locations).
- Added a warning message to summary.cross for the case that there are
chromosomes > 1000 cM in length (which might indicate that they're
really in basepairs).
- Revised pull.map to have argument as.table; if as.table=TRUE the map
is returned as a simple table with chromosome assignments and
positions.
- Revised fill.geno to have a third option, method="no_dbl_XO", which
fills in missing genotypes between markers with exactly the same
genotype.
- Revised est.map so that the output with verbose=TRUE is less verbose
and more informative.
- Changes in C++ code, to fix problems that prevented the package from
being compiled on Solaris.
## Version 1.15, 5/2/2010:
### Major changes:
- In collaboration with Danny Arends, Pjotr Prins, and Ritsert Jansen,
we have incorporated Ritsert Jansen's MQM mapping software within
R/qtl. (Previously, it was available only through the commercial
software package, mapqtl). See the tutorial at
https://rqtl.org/tutorials/MQM-tour.pdf
### Minor changes:
- Added a function transformPheno for transforming one or more
phenotypes in a cross object.
- Added a function convert.map for converting a genetic map from one
map function to another.
- Added functions convert2riself and convert2risib, for converting a
cross object to be treated as RIL by selfing or sib mating,
respectively.
- Added function simulateMissingData, for omitting genotypes at random
from a cross object.
- Revised write.cross so that it can handle non-numeric phenotypes.
Also changed the default for the "digits" argument to NULL, so that
phenotypes and map positions are not rounded.
- Revised read.cross to have arguments error.prob and map.function, to
be used if est.map is called.
- Revised locateXO: it no longer shifts the first marker to position
0, and it has a new argument, full.info; if this is TRUE,
the output includes not just the estimated crossover locations but
also the endpoints of the intervals to which they are known to reside.
- Revised summary.cross so that if there are > 30 phenotypes, we don't
show the percent missing phenotypes for all traits but just overall.
- Revised stepwiseqtl so that if additive.only=TRUE, you only need to
give one penalty.
- Revised read.cross with format="csv" so that initial fields in 2nd
row need not be completely empty, but can have white space. (This
was a common problem for users importing csv files.)
- In plot.qtl, added argument "justdots", so that one can plot just
dots at the QTL rather than arrows and QTL names, and "col", the
color used to indicate the QTL.
- Fixed a bug in xaxisloc.scanone for the case of multiple chr/pos in
the input.
- Fixed an apparent bug in read.cross for format="qtlcart"; need to
treat negative genotype codes as missing.
- Fixed a bug in sim.cross for type="4way"; previously it was just
using the female map for both female and male meioses.
- Fixed a bug in find.pseudomarkerpos in the case of sex-specific maps
(as in a 4-way cross).
- lodint and bayesint now stop with an error if chr or qtl.index have
length > 1. Before, they gave weird results and a meaningless
error.
- In read.cross with format="csv", give a better error message if
there are odd values in the marker positions.
- Fixed a bug in scanone/scantwo for RIL on the X chromosome; the X
chromosome needs to be treated like to autosomes. We can't really
deal with the sexes properly here.
- Revised scanone and scantwo so that, if using multiple CPUs via snow
and calculations are stopped early, the cluster nodes are stopped on
exit.
- Revised summary.cross so that, for cross type "riself", there's no
warning about a chromosome named "X" having class "A".
- Removed some odd erroneous code from the plot.qtl function.
- Fixed a bug in summary.scanone that shows up in the case of multiple
LOD columns with permutations and format="allpeaks".
- Fixed a bug in scanone permutations in the case of multiple
phenotypes with missing data.
- Fixed a problem in effectplot that arose from an apparent bug in
weighted.mean in R version 2.10.1
## Version 1.14, 9/30/2009:
### Major changes:
- None.
### Minor changes:
- Slight changes to read.cross for formats "mm" and "qtlcart",
regarding use of the function grep().
## Version 1.13, 9/10/2009:
### Major changes:
- Fixed a bug in fitqtl regarding the case of a locus on the
chromosome...the cited LOD scores for X chromosome loci were not
right. Had to make slight modifications to scanqtl, addqtl,
addpair, addint, addcovarint, refineqtl.
### Minor changes:
- Revised makeqtl, addtoqtl, dropfromqtl, replaceqtl, and reorderqtl
so that qtl objects now include a "chrtype" component, indicating
whether QTL are autosomal or for the X chromosome.
- Revised scanone and scantwo for multiple phenotypes with missing
data so that, with method="hk" or method="imp", the phenotypes are
grouped into batches with matching patterns of missing data, rather
than just doing each one at a time.
- Added a function locateXO (formerly the internal function locate.xo)
to estimate the locations of crossovers on a given chromosome.
- Added a function, c.scantwo (aka cbind.scantwo), for concatenating
multiple scantwo results.
- Revised summary.map to deal with the case of a single marker on a
chromosome.
- Revised scantwo so that phenotype names are in dimnames of the lod
component of the output.
- Fixed bugs in read.cross with format="mm" to deal with changes to
grep. [replaced grep("^*", ...) with grep("^\\*", ...)]
- Fixed a bug in reorderqtl; the n.gen component was not getting
fixed.
- Fixed a bug in switch.order; results of est.rf were getting messed
up.
- Fixed some minor issues regarding hyperlinks in help files.
## Version 1.12, 6/30/2009:
### Major changes:
- Added the ability to simulate RIL and multiple-strain RIL in the
sim.cross function. For the case of multiple-strain RIL, one needs
genotype data on the founder strains, which may be simulated with
the new function simFounderSnps. The encoding of genotypes in
multiple-strain RIL is quite complicated. See the help file for
sim.cross.
- Added the ability to deal with 4- and 8-way RIL in calc.genoprob,
sim.geno, argmax.geno, est.map, ripple, est.rf, tryallpositions,
calc.pairprob, and calc.errorlod.
- Added a function, readMWril, for reading data on 4- or 8-way RIL.
- Fixed a minor problem in read.cross, with format="csv", in the case
of many phenotypes that resulted in *really* slow data import. (To
read a file with 200 individuals and 1500 phenotypes, it would take
about 60 seconds and now takes about 2 seconds.)
- Added the ability to have scanone and scantwo permutations run in
parallel, if the snow package is installed. The added argument
n.cluster indicates the number of parallel nodes to use.
### Minor changes:
- Added a CITATION file; type citation("qtl") within R to get
information on the citation to use in articles that make use of
R/qtl.
- You can now subset crosses with brackets, [ ], as with a matrix with
rows=chromosomes and columns=individuals. See the examples in the
help file for subset.cross.
- Added a utility function, findDupMarkers, for identifying groups of
markers with identical genotype data. (This is useful for reducing
the genotype data in the case of a very high marker density.)
- Added a utility function, xaxisloc.scanone, for finding x-axis
locations for given genomic positions in a plot of scanone results
(useful for adding annotations, such as text or arrows).
- Added functions subset.map and `[.map` for pulling out selected
chromosomes from a map object.
- The output of tryallpositions, for testing possible positions for a
genetic marker, now has class "scanone", so that one may use
plot.scanone, summary.scanone, etc.
- Added an argument mark.diagonal to plot.rf(), to include black lines
segments around the pixels on the diagonal. This helps to separate
the upper left triangle from the lower right triangle.
(The default is FALSE.)
- In geno.crosstab, the first argument (mname1) can now be a vector
with the two marker names; in this case, mname2 should be missing.
- Revised clean.scantwo so that, by default, positions must have at
least one marker *in between* them. Added arguments n.mar
(no. markers that must separate two positions) and distance (cM
distance between two positions). These arguments were also added to
scantwo (as clean.nmar and clean.distance).
- Revised summary.scanone and summary.scantwo so that the perms
argument can contain a single column of permutation results, in
which case they are assumed to apply to any LOD score columns.
- Revised summary.scanone so that the perms argument can be
scantwo permutations results; added an internal utility function,
scantwoperm2scanoneperm, for pulling the scanone permutations out of
the scantwo permutations.
- In plots of output from addpair with a special formula, plot.scantwo
now gives just one set of numbers on the color scale.
- Fixed a bug in plot.scanone that shows up if the "chr" column is not
a factor. Now we convert the column to a factor in advance.
- Fixed a bug in stepwiseqtl in the case that the inferred model
contains no QTL; deparseQTLformula needs to deal with the NULL case.
- Fixed a bug in c.cross regarding "map" attributes in $prob or $draws.
- Fixed a bug in cim() [reported by Sandy Taylor] that occurred in the
case of multiple marker covariates within a window (and >3 marker
covariates on that chromosome.
- Fixed a bug in summary.scantwo in case that scanoneX component is
numeric(0) and not NULL, which resulted in a major crash.
- Revised +.scantwo and -.scantwo so that if the scanoneX component in
the input is NULL, the output has scanoneX that is NULL.
- Fixed a bug in addpair() in the case that the user gives a formula
that includes one but not both of the new QTL.
- Revised ripple() to give a warning message if the chr argument is
not provided.
- In compareorder(), switch.order(), and ripple(), changed the default
value for the tol argument to 1e-6 (as in est.map).
- Slight change in compareorder() so that the order argument can be of
length n.mar+2, but with only the first n.mar items considered.
- Slight change in checks of chr argument in ripple and switch.order;
added a function testchr for checking that a chromosome argument is
okay.
- In the output of c.cross, there is a numeric phenotype "cross" that
indicates which individuals are from which cross, as a single
column.
- Revised fixXgeno.f2 so that warnings are given the appropriate
allele labels (if they are provided to read.cross).
- Fixed a few problems in c.cross regarding the attributes to
QTL genotype probabilities and imputated genotypes
- Added a function chrnames, for pulling out the chromosome names from
a cross.
- Revised the software license to the GNU General Public License,
version 3.
- Minor change in plot.cross so that if one types plot(mycross, mymap)
it is shipped to plot.map rather than giving an error message.
- Revised the R/qtl tutorial to refer specifically to the GPL v3.
## Version 1.11, 3/29/2009:
### Major changes:
- Revised effectplot so that one may refer to "pseudomarkers" by their
chromosome and position with a construction like "5@32.8", rather
than having to first call find.pseudomarker to get the name. Also,
in the actual plot, we use the form "5@32.8" rather than, for
example, "c5.loc47".
### Minor changes:
- Revised the software license statements throughout the source code
(and above), for clarity and consistency.
- Revised write.cross so that it may write doubled haploid (type "dh")
data.
- Fixed a problem with movemarker regarding the treatment of
chromsome names.
- Slight change to makeqtl so that QTL names of the form "5@30.0" have
ending 0's left in, if appropriate (so that if one QTL is referred
to as "1@12.23", then another like "5@30" will be given as
"5@30.00", so that all have equal precision.
- Added a function find.pseudomarkerpos for finding the position
corresponding to a "pseudomarker" name (similar to find.markerpos).
- Added an internal function charround() for rounding numbers, turning
them into character strings with ending 0's preserved.
- Fixed a slight bug in lodint() regarding the case of multiple
positions sharing the maximum LOD score.
- In dropfromqtl, addtoqtl, replaceqtl, and reorderqtl, attributes
"formula" and "pLOD" are now stripped.
- In replaceqtl, changed the argument "indextodrop" to just "index",
as in dropfromqtl.
- Added a more clear error message in plot.map in the case that a
sex-specific map and a sex-averaged map are input.
- In plot.info and plot.geno, we now allow one to use main as an
argument for producing a self-defined title.
- Slight change in plot.qtl, regarding placement of text and size of
arrows.
- In summary.fitqtl, print.addint, and print.addcovarint, eliminated
an extraneous blank line after the model formula.
- Added code from Pjotr Prins enabling R/qtl to be linked against Perl
and Ruby, as part of biolib.
## Version 1.10, 1/11/2009:
### Major changes:
- Revised the way that the 'chr' argument is treated in functions such
as scanone, scantwo, etc., to give greater consitency. Numbers are
interpreted as character strings to be matched to the chromosome
names. Negative numbers and character strings that start with "-"
are interpreted as omitting the corresponding chromosomes, matched
by name. One may also use a logical vector (TRUE/FALSE), of the
same length as there are chromosomes, indicating which chromosomes
are to be considered. So if an object has three chromosomes named
"1", "3", "4", using chr=2 will result in an error, while chr=3 will
give the second chromosome (named "3").
- Also revised the way that the 'ind' argument is treated in
subset.cross and plot.geno, in the case that the input cross
contains individual identifiers in the phenotype data. The 'ind'
argument can still be a logical vector, but otherwise we first seek
to match the values against individual identifiers. For identifiers
that are character strings, one may use "-" at the beginning of each
to indicate all individuals except those given.
- Added an argument 'batchsize' to scanone and scantwo, so that in the
case that multiple phenotypes (or permutations) are to be run as a
batch (with method "hk" or "imp"), they can be run in smaller
batches (indicated by batchsize). This can speed things up quite a
bit in the case of a very large number of phenotypes (or
permutations).
- Added two functions for the de novo construction of a genetic map.
formLinkageGroups uses pairwise marker linkage information
(calculated with est.rf) to partition markers into linkage groups.
orderMarkers uses a quick but not very good algorithm for ordering
the markers on a chromosome (minimizing the number of obligate
crossovers).
- Added a function addcovarint, which is similar to addint, but adds
one QTL x covariate interaction at a time.
### Minor changes:
- Created functions replacemap.scanone and replacemap.scantwo, which
enable one to plot scanone or scantwo results relative to another
map (with positions interpolated based on marker locations). These
can be used, for example, so that one may plot scanone or scantwo
results relative to a physical map.
- Added a function replacemap.cross, which is the same as the long
extant function replace.map. This was so that I could the functions
replacemap.scanone and replacemap.scantwo (see above). All can be
used with the 'generic' function replacemap.
- Revised the functions nchr, nmar, totmar, so that they work for map
objects as well as cross objects. Separated the help files for
nind, nmar, totmar, nphe, nchr from the summary.cross help file, so
that the use of the revised functions can be explained.
- Revised the way in which LOD score columns are renamed in c.scanone
and cbind.scanoneperm. If labels are given, these are appended to
the end of the names, but if labels are not given and there are no
repeats in the column names, the column names are left as they were.
- Added functions subset.scanoneperm and subset.scantwoperm for
pulling out selected LOD columns in the case that permutation tests
were run with multiple phenotypes.
- Revised calc.penalties so that it can deal with the case of scantwo
permutations for multiple phenotypes: Added an argument "lodcolumn"
for selecting the phenotype; if missing, penalties for all phenotype
are calculated.
- Added a function markernames for pulling the marker names out of a
cross object (as one long vector).
- summary.cross now checks for duplicate chromosome names and
chromosome names that start with '-', either of which would cause
major problems.
- Revised summary.cross so that, if the phenotype data are missing
column names, an error is given.
- Revised est.map so that the chromosomes are given classes "A" or "X"
according to the chromosome types in the input cross object.
- Revised geno.crosstab to deal with partially informative genotypes
in an intercross or 4-way cross. Added an argument so that (by
default) columns and rows with no data will not be printed.
- Revised comparegeno to have the option what="both", through which
the result has the proportion of matches in the lower triangle and
the number of matches in the upper triangle. Also, now if
what="proportion" the diagonal has all missing values (rather than
all 1's); otherwise the diagonal contains the number of typed
markers for each individual.
- Revised movemarker so that one can move a marker onto a totally new
chromosome.
- Revised sim.cross so that if the input map object has no chromosome
names, the chromosomes in the output cross object still have names.
- Revised summary.cross to give a warning if the chromosomes are not
named.
- Added a function convert2sa for converting a sex-specific map object
to a sex-averaged map object by pulling out the female marker
locations (and issuing a warning if the female and male locations
are very different). This is useful for plotting a simpler version
of a map estimated for a 4-way cross via est.map with sex.sp=FALSE.
- Slight change to countqtlterms(), used by stepwiseqtl(), to skip the
parsing of interactions in the case that there are 0 or 1
interactions; this might speed things up slightly.
- Fixed a slight with plotModel; the lines indicating interactions
were a bit askew.
- Slight changes in ripple and bayesint, changing use of rev(order(.))
to order(., decreasing=TRUE)
- Added a more clear error message in the case that the number of
individuals in the cross doesn't match the number of individuals in
the QTL object in fitqtl, stepwiseqtl, addqtl, addint, addpair,
refineqtl.
- Fixed a couple of bugs in refineqtl, one concerning convergence and
the other concerning dropping individuals with missing covariates or
phenotypes in the case that there is just one covariate.
- Fixed a slight problem in c.cross: if maps are not precisely the
same, we don't try to combine the genotype probabilities.
- Fixed a bug in summary.scanone with format="allpeaks" for the case
that there are no peaks meeting the threshold/alpha.
- Fixed a bug in switch.order related to the change in references to
chromosomes.
## Version 1.09, 7/18/2008:
### Major changes:
- Added a function stepwiseqtl() for performing forward/backward
selection to identify a multiple QTL model, with model choice made
via a penalized LOD score, with separate penalties on main effects
and interactions.
- The documents "Brief tour of R/qtl" and "New functions for exploring
multiple-QTL models" were revised to discuss the stepwiseqtl
function.
- calc.penalties() uses permutation results for a 2-dimensional, 2-QTL
scan to derive penalties for the penalized LOD scores used by
stepwiseqtl().
- plotModel() is a new function for creating a simple graphical
representation of a QTL model.
- Added an additional cross type, "dh", for doubled haploids. This is
treated like a backcross, though genotypes will be indicated as
homozygotes. Changed a whole bunch of functions very slightly to
accommodate this.
- The argument pheno.col in many functions can now be a vector of
numeric phenotypes. This could be useful for studying the results
with various transformations of a phenotype. The vector has to be
numeric, has to have the length equal to the number of individuals
in the cross, and has to contain either non-integers or values
outside the range 1,2,3,...n.phe. (The revised functions are
scanone, scantwo, addqtl, addint, addpair, cim, effectplot, fitqtl,
plot.pxg, plot.pheno, refineqtl, scanoneboot, scanqtl, stepwiseqtl.)
- lodint and bayesint were revised to accept qtl objects output by
refineqtl (with keeplodprofile=TRUE). An additional argument,
qtl.index, was added to indicate for which QTL (within such qtl
objects) the approximate confidence intervals should be derived.
For scanone output, the functions were modified so that, if the
results concern just a single chromosome, the chromosome argument is
not needed.
- In refineqtl, the default for the argument keeplodprofile is now
TRUE. The LOD profiles contained in the output of refineqtl are now
of class "scanone".
### Minor changes:
- Covariates (argument covar) in fitqtl, scanqtl, addqtl, addpair,
addint, and refineqtl can now be a numeric matrix (with column
names), and not just a data.frame.
- Permutation results obtained via scantwo now include the maximum LOD
score from a single-QTL scan. This is not used in summary.scantwo,
but is included for completeness.
- Added an argument 'pvalues' to summary.fitqtl and addint; if FALSE,
the pvalues are not displayed.
- Added a function ntyped() which is just like nmissing() except it
gives the opposite thing (no. genotypes per individual or marker).
- est.rf, for a backcross, had been replacing estimated rec frac > 0.5
with 0.5. This is no longer done.
- The print and summary function for QTL objects now will print the
formula and penalized LOD ("pLOD") if they exist as attributes.
They also take into account the case of a null QTL model.
- Revised makeqtl so that QTL names are of the form "1@15.0" rather
than "Chr1@15.0"; the "Chr" seemed gratuitous.
- Changed some of the examples in the help files to use pull.pheno in
place of references to cross$pheno.
- Revised summary.cross so that it pays attention to options("width")
and prints things more nicely if there are loads and loads of
phenotypes or whatever.
- We now allow formulas in fitqtl, refineqtl, addqtl, etc., to be
character string representations of formulas. (They are then
converted.)
- Added a function cbind.scanone (which is identical to c.scanone).
- The output of fitqtl now includes an element "lod" containing the
LOD score from the fit of the full model.
- In reorderqtl, if the argument neworder is not provided, the QTL are
ordered by chromosome and then by position within a chromosome.
- We define a new class, "compactqtl", for defining the trace through
model space in stepwiseqtl() (if called with the argument
keeptrace=TRUE). This is similar to the class "qtl" (of QTL objects
created by the makeqtl() function), but containing just chromosome
IDs and positions of QTL.
- Fixed a bug in effectplot in the case that not all possible
genotypes are observed in the imputations.
- Slight change in plot.scanone so that one may use xlab as an
argument. Similarly changed plot.map so that one may use xlab and
ylab to change the x- and y-axis labels. Similarly changed
plot.scantwo so that one may use xlab and/or ylab to change the x-
and y-axis labels. (In plot.scantwo, if just one of xlab or ylab is
given, the other is assumed to be the same.)
- Slight change to summary.fitqtl and summary.addint so that very long
formulas are split across multiple lines.
- Slight change to scanqtl to avoid going just outside the defined
intervals (specifically, so that refineqtl and plotLodProfile do not
go just past the flanking QTL).
- Slight change in plot.scantwo to avoid affecting par("mfrow") or
par("mar") in the case zscale=FALSE. Also fixed a slight bug
regarding "any(contours)>0" vs "any(contours>0)".
- Slight change in the way refineqtl determines convergence, to try to
avoid unnecessary iterations.
- Slight change to plot.scanone so that the chr argument can be logical.
- Simplied code for 'cat' statements in many places; we'd used
cat(paste(...)) and the call to paste wasn't needed.
- Fixed an error in scanqtl that arose if there are multiple markers
at the same position. Now give a warning message.
- The title of the plot produced by plot.rf can now be modified by
including the argument 'main' in the call.
- In plot.geno, if chr is missing, we plot the genotypes for the first
chromosome. Changed the label "Position (cM)" to "Location (cM)"
(just for consistency across functions).
- In geno.crosstab, changed the column and row labels for missing data
from "NA" to "-".
- Made a slight change to plot.pxg regarding the locations of the
genotype labels on the x-axis.
- Revised print.map so that it doesn't print the log likelihood
attribute.
- Fixed a bug in addpair if the formula is missing.
- Fixed a bug in est.rf for 4-way crosses.
- Fixed a bug in c.scanoneperm, c.scanone, and c.scantwoperm regarding
the "df" (degrees of freedom) attributes.
- Fixed a bug in read.cross with format "csv" (or "csvs" or "csvr" or
"csvsr") so that dec="," can be used as an argument.
- Fixed a potential bug in read.cross with format "mm" for pulling out
the cross type.
- Fixed a bug in add.threshold for the case of multiple phenotypes.
- Fixed a bug in scanone permutations in the case of a single
covariate with some individuals with missing phenotypes and/or
covariates.
- A more meaningful error message is given in makeqtl in the case that
multiple markers are at identical positions, so that qtl locations
cannot be determined.
- Fixed a bug in read.cross with format="csvs" or "csvsr" for the case
that there are individuals with phenotypes but no genotypes.
- Fixed a bug in refineqtl for the case of linked QTL. (Incorrect
limits for the search intervals were used.)
- Fixed a bug in plotLodProfile for the case of linked QTL. (LOD
profiles were not placed correctly.)
- Slight change to the internal function reviseqtlnuminformula(),
so that the input formula can be a character string.
- Fixed slight bug in scanone and scantwo [any(weights)<=0 changed to
any(weights<=0)]. Fixed a similar bug in plot.geno [any(errors)
changed to any(errors != 0)].
## Version 1.08-56, 4/8/2008:
- Fixed a bug in scanqtl.
## Version 1.08-55, 4/3/2008:
### Major changes:
- For all functions taking a "pheno.col" argument (including scanone
and scantwo), this argument can now be a character string indicating
the name of a phenotype. (Previously, it had to be a numeric index
indicating the phenotype).
- fitqtl now takes a cross object and pheno.col (as with scanone,
scantwo and scanqtl), rather than a column of phenotypes.
- Implemented Haley-Knott regression for the fit of multiple-QTL
models in fitqtl and scanqtl.
- Added functions addint, addqtl, and addpair, for exploration of
multiple QTL models. addint tries adding all possible pairwise
interactions, one at a time, to a multiple QTL model. addqtl scans
for an additional QTL to be added to a multiple QTL model. addpair
scans for an additional pair of QTL to be added to a multiple QTL
model.
- Added functions addtoqtl, dropfromqtl, and replaceqtl, for
manipulating a qtl object created by makeqtl().
- Added a function refineqtl(), for getting the maximum likelihood
estimates of QTL positons (as best we can) in the context of a
multiple-QTL model. Added a function plotLodProfile which can
create a figure with 1-dimensional LOD profiles for each QTL, in the
context of a multiple QTL model, as is commonly created for multiple
interval mapping.
- Added a function, tryallpositions(), for testing all possible
positions for a given marker, keeping the order of all other markers
fixed.
- Added a function, compareorder(), for comparing a given order of
markers on a single chromosome to the current one contained within a
cross object.
- Added some additional marker genotype codes for the phase-known
4-way cross, for a dominant marker with both parents being
heterozygous: 11 = not AC, 12 = not BC, 13 = not AD, 14 = not BD.
- Revised est.rf, for estimating recombination fractions between all
pairs of markers, so that it can give results for many of the
incompletely informative markers in a 4-way cross.
### Minor changes:
- Added an additional argument (expandtomarkers) to lodint, bayesint,
and summary.scanoneboot. If TRUE, the intervals provided are
expanded to the nearest flanking markers.
- Added a function geno.crosstab for creating a cross-tabulation of
the genotypes at two markers.
- Added a function pull.pheno for pulling out the data for a phenotype
or phenotypes.
- Added a function countXO for counting the number of obligate
crossovers for each individual across the genome or on individual
chromosomes.
- Added a function plot.qtl, for plotting the locations of QTL in a
qtl object against the genetic map.
- Added a function checkformula for checking the formula in
fitqtl/scanqtl, to ensure that it satisfies the hierarchical
structure we assume: if a term is involved in an interaction, its
main effect should also be included.
- Added an additional argument to fitqtl, run.checks. If TRUE, we
check the input formula and look for individuals with missing
phenotype or covariates. This is included so that the checks are
not repeated multiple times when scanqtl calls fitqtl.
- Added the ability to calculate joint QTL probabilities assuming
conditional independence of QTL genotypes given markers genotypes.
(An approximation, but it speeds up scantwo slightly, for a chr
versus itself.) Added an argument assumeCondIndep to scantwo().
- Added an argument "zmax" to the plot.rf function, for controlling
the color scale of LOD scores. Values at zmax are red; values above
zmax are thresholded at zmax.
- Added functions plot.scanoneperm and plot.scantwoperm for plotting
histograms of the permutation results from scanone and scantwo.
- Added a function plot.scanoneboot, for plotting a histogram of the
results of scanoneboot.
- scanoneboot now stops with an error if the argument pheno.col
indicates multiple phenotypes.
- Revised find.marker to have an argument "index" which may be used in
place of the "pos", to find marker names by their numeric order
within a chromosome rather than by map position.
- In read.cross, with formats "csvs" or "csvsr", we now allow that
some individuals have phenotypes but no genotypes and vice versa,
and the individuals in the genotype and phenotype files are not
required to be in the same order.
- In the getsex() function, for pulling out sex and pgm for all
individuals, we now attempt to infer the status of individuals with
missing information. Warnings are given.
- Fixed a bug in read.cross.qtx, concerning the case that genotypes
are like H:B or A:B, and need to be converted to A:H.
- Fixed a bug in effectscan for the X chromosome in the case of an
intercross with both directions but just one sex.
- Slight change to plot.geno() to make individual IDs shown rather
than just numbers, if they are available.
- Slight change to effectscan, to pass the "..." argument to the plot
function, so that, for example, you can use the 'main' argument to
put a title on the plot.
- Slight changes to top.errorlod() and getid() to deal with a bug for
the case that there is an "ID" phenotype column with names like
"1_F1".
- Fixed some code in scanqtl regarding dropping individuals with
missing phenotypes and/or covariates that really slowed things
down. Revised the analogous code in fitqtl.
- Added an argument to est.map: omit.uninformative. If TRUE (which
is the default, and which was previously the only option),
individuals with fewer than two typed markers are omitted. This was
added for use by the new function tryallpositions().
- Added a function markerloglik, for calculating the log likelihood
for a fixed marker. This was added for the use of the new function
tryallpositions().
- read.cross now prints the cross type at the end.
- read.cross (with format="mm" or one of the "csv" formats) gives a
more explicit warning message if phenotypes are to be treated as
missing.
- Revised summary.qtl to also indicate the number of imputations, in
the case that the qtl object contains them.
- cim() had previously used a single column for each covariate in an
intercross (that is, it assumed additivity of alleles); this is
fixed: it now uses two columns. A revised forward selection
algorithm for intercrosses was written, to select these pairs of
columns together.
- Fixed a slight bug in lodint and bayesint that changed the marker
names if the LOD peak was at one end of the interval.
- subset.scantwo will now drop X chromosome related stuff from the df
attribute if the X chromosome has been omitted.
- Changed the default tolerance in est.rf and est.map to 10^-6 (rather
than 10^-4). Increased the default maxit (maximum no. iterations)
to 10000.
- Added an extra column in the results of summary.map, giving the
maximum distance between markers on each chromosome and overall.
- QTL objects produced by makeqtl now include a component "altname",
which will be like "Q1", "Q2", ... Changed fitqtl to look at this
rather than at the column names of qtl$geno.
- Made a slight change to plot.scantwo regarding z-limits when zlim
is missing and allow.neg=TRUE.
- The objects of class "scanoneperm" and "scantwoperm" now have a
secondary class (either "matrix" or "list")
- Fixed a bug in scantwo perms for the use of the argument clean.scantwo.
- Fixed a bug in summary.cross in the case of invalid genotypes in a
cross.
- Fixed a slight bug in subset.cross regarding the recombination
fractions from est.rf().
- Fixed slight bugs in effectplot and reviseXdata regarding the X
chromosome in an intercross with both sexes and one cross direction.
- Fixed a bug in CIM for the case of multiple marker covariates on the
same chromosome.
- Fixed a bug in revisecovar() regarding dropping of covariates for the X
chromosome.
- Fixed a bug in add.threshold.
- Fixed a bug in movemarker for the case of sex-specific maps and
with the marker being moved to the middle of a chromosome with
exactly two markers.
- Fixed a bug in geno.table; missing genotypes weren't shown for the X
chromosome.
- Fixed a bug in fit.stahl.
- Subtle modification to a few of the help pages to conform to a
change in R.
- Changed the default for plot.geno back to a horizontal plot
(horizontal=TRUE); changing it to vertical was a bad idea. Fixed a
slight bug regarding F2-type markers in 4-way cross.
- In write.cross with the "qtlcart" format, if there is a previous
file that would otherwise be overwritten, it is now moved to a file
with extension ".bak" rather than ".mov". Also made some slight
revisions to get things in the map file to line up.
- Made a minor change to plot.map, so that if the "..." contain xlim
or ylim, they are used in place of the defaults.
## Version 1.07, 9/20/2007:
### Major changes:
- Completely rewrote the effectscan function, so that it now uses
multiple imputation results and deals with the X chromosome
appropriately.
- Fixed an important bug in fitqtl, in which incorrect results could
be obtained if covariates were placed before QTL terms in the
formula.
### Minor changes:
- Added an argument "alternate.chrid" to plot.scanone, plot.scantwo,
plot.info, plot.missing, geno.image, plot.map, plot.cross,
effectscan, plot.errorlod, and plot.rf. If TRUE, the placement of
chromosome ID axis labels is alternated, so that they may be more
easily distinguished. For plot.cross, alternate.chrid=TRUE has been
made the default; for the other functions, FALSE is the default.
- In the output from makeqtl, "pos" is now the precise position of the
pseudomarkers (rather than just the input values), and the QTL names
reflect that (though they are rounded). replaceqtl and addqtl were
similarly revised.
- In makeqtl, added an argument what=c("draws","prob"); we now pull
out either the results of sim.geno or the results of calc.genoprob,
and not both. (Only the former is needed at this point; the latter
will be used once we have implemented EM/HK/eHK in fitqtl.
- plot.geno now works for a 4-way cross; we changed the default to be
a vertical plot (ie, horizontal=FALSE).
- Added functions print.qtl, summary.qtl, print.summary.qtl, for
getting simple information about a QTL object.
- Fixed slight bugs in pull.map and replace.map.
- Fixed a slight bug in top.errorlod, for the case that there are IDs
(e.g., in cross$pheno$id) that are not numeric.
- Fixed a slight bug in scanqtl.
- Changed checks regarding the class of the input to various functions
to be a bit more permissive.
- Fixed a potential problem (which shouldn't be realized) in reviseXdata.
## Version 1.06, 8/7/2007:
### Major changes:
- Revised the method for calculating genotyping error LOD scores. For
each individual and each marker, the error LOD score is calculated
assuming that all other genotypes for that individual on that
chromosome are correct. The new procedure requires much more
computation time (especially in the case of dense markers), but
identifies many additional potential errors. A new argument,
version, allows one to specify use of the "new" or "old" version of
the error LOD score calculations.
- Added a function geno.image for plotting an image of the genotype
data. This is much like plot.missing, but gives the genotypes in
color, rather than just black/white indicating missing/not.
- Revised geno.table so that it gives reasonable p-values for the X
chromosome and for the case of dominant markers in an intercross.
Added a chr argument to obtain results for only selected
chromosomes.
- Added a function cim() for performing composite interval mapping by
one of the schemes used in QTL Cartographer: forward selection at
the markers, to a fixed number of markers, followed by interval
mapping using those marker as covariates, and dropping any markers
within some fixed window around the position under test. The
results may be plotted or summarized using the functions for output
from scanone(). Also added a function add.cim.covar, for adding
dots, to a plot from plot.scanone(), to indicate the selected marker
covariates.
- Extended the code for fitting the Stahl model for crossover
interference to the case of intercross data. (Modified the
functions est.map and fitstahl, and the underlying C code.)
- Added functions scanoneboot and summary.scanoneboot, for deriving
bootstrap confidence intervals for the location of a QTL, but we
recommend using lodint or bayesint, instead.
### Minor changes:
- Added a function find.markerpos(), for finding the chromosome and
position of a marker (or vector of markers).
- Added arguments 'xlab', 'ylab', and 'col' to effectplot(), so that
you can override the defaults.
- Added a function add.threshold() for adding a significance threshold
(estimated via permutation results) to a plot created by
plot.scanone().
- Revised plot.pxg() so that unobserved genotypes will not be
displayed. This was needed for the plot of two-locus genotypes on
the X chromosome.
- Changed the names in two of the columns in the output from the 2d
permutation test, to be "fv1" and "av1" rather than "2v1.int" and
"2v1.add", to correspond more closely to the names in the
summary.scantwo output. Also, we now allow the argument "alphas" to
be a single number, in which case it is assumed that the same
significance level is to be used for all five LOD scores.
- Made a slight change in summary.scanone(), so that when p-values are
provided, the rownames don't get lost.
- Revised the hyper data set slightly; changed the "alleles"
attribute, to be c("B","A") rather than c("A","B"), as this was a
backcross to the B strain.
- In scanqtl, if no a fixed model (with no scanning) is fitted, the
output is now just the LOD score for that fitted model.
- clean.cross was dropping any "alleles" attribute; this is now fixed.
- Added a "lodcolumn" argument to lodint() and bayesint().
- Fixed a bug in scanqtl; in two-dimensional scans, the first row of
the results was wrong.
- Fixed a bug in c.cross concerning combining backcross and
intercrosses.
- Fixed a bug in effectplot() regarding pseudomarkers with names like
"c3.loc42.5".
- Fixed a bug in discan, for the case of method="mr".
- Fixed a bug in write.qtlcart regarding RIL.
- Fixed a bug in max.scanone for the case that there is more than one
locus with the maximum LOD score. (In that case, we print a random
locus, among those having the maximum LOD.)
- Revised summary.scanone so that the rule is to pick out LOD scores >
(rather than >=) the threshold.
- Revised -.scanone, -.scanoneperm so that very small differences get
set to 0.
- Added ability to halt calculations via Ctrl-c in many of the C
routines. (Previously, you'd have to wait for an exit from the C
code.)
- There was a bug in sim.cross() regarding the QTL effects for a
backcross.
- Fixed a bug in drop.markers, for a 4-way cross.
- Fixed a bug in est.map, for a 4-way cross and the case of
sex-averaged maps.
- Made a slight change regarding estimating rec fracs in 4-way cross
(possibly immaterial).
- A slight change in the C code for imf_stahl.
- Modified locate.xo() slightly...when there is no crossover, it
gives numeric(0) rather than NULL.
- Fixed a slight problem with the format of the degrees of freedom in
scanone permutation results.
- Slight change in the color scheme in effectplot()
- Fixed a slight bug in fitstahl() that made it crash if none of
m, p, and error.prob were specified. Also revised the function so
that we look only for error.prob <= 0.5.
- Fixed a slight bug regarding sex-specific maps in the create.map()
function.
- Slight revision in plot.geno, so that if the "ind" argument contains
duplicates of individuals, only the unique individuals are
plotted.
- Slight revisions to scanone, scantwo, and discan, so that, in the
midst of permutations, just one instance of various warnings is
printed.
- Changed the names of some of the sample data files.
- Revised the fitstahl function to use of the estimated map for one
value of m as the starting point for the next value. This can
really cut down on the required EM iterations and so speeds things
up.
- In the "map" component of the output from scantwo, the name of the
second column is now "pos" rather than "map", to correspond more
closely to the scanone output (and because it is more appropriate).
- Fixed a bug in write.cross; in an intercross with all males and all
pgm==1, all X chromosome genotypes got converted to AA.
- Added a few more verbose error messages in read.cross for the "csvs"
format (contributed by Steffen Moller, University of Lubeck).
- Fixed a slight bug in scanone with model="2part" or model="binary",
that showed up if one first used jittermap().
- Added arguments maxit, tol and sex.sp to switch.order()
- Fixed a bug in movemarker() for the case of a 4-way cross.
- In write.cross.gary(), changed a couple of uses of 'T' and 'F' to
'TRUE' and 'FALSE', respectively.
- Fixed find.markerpos so that it works with a 4-way cross.
- Revised plot.scantwo so that the upper and lower arguments can take
values "fv1" and "av1" as aliases for "cond-int" and "cond-add",
respectively.
## Version 1.05, 11/8/2006:
### Major changes:
- Fixed a problem with permutations in scanone and scantwo: covariates
weren't being permuted to match the phenotypes.
### Minor changes:
- Fixed a slight bug in scanone for model="binary".
- Revised write.cross for the "qtlcart" format; there was a problem in
the case that there were many markers on a chromosome.
- Revised the C code for imf_stahl, to better deal with void pointers.
## Version 1.04, 10/28/2006:
### Major changes:
- R/qtl has a new web site: rqtl.org
- Revised the format for the output from scantwo. Added a function
convert.scantwo for converting from the previous format to the new
format. For scantwo results calculated with R/qtl version 1.03 and
earlier, you'll need to use convert.scantwo to convert them to the
new format in order to use the summary.scantwo and plot.scantwo
functions. (In the previous format, joint and epistasis LOD scores
were stored; now we store the joint LOD and the LOD from the
additive QTL model. This is so that, if there is a problem with the
joint model, it won't corrupt the results for the additive model.)
- Eliminated the 'run.scanone' argument from the scantwo() function.
scanone is always run. The summaries and permutation tests require
these results.
- plot.scantwo now has an 'upper' as well as a 'lower' argument, for
complete control over what gets plotted.
- Completely revised the summary.scanone and summary.scantwo
functions. I have written documents to explain the use of the new
functions. These are distributed with the code and are also
available at the R/qtl website (https://rqtl.org), under
"Tutorials".
- summary.scanone: There is now a format argument, useful for the
case that the scanone result contains multiple LOD score columns
(for example, for multiple phenotypes). We may focus on a single
LOD column (format="onepheno"), as was done before; include
different rows for the peaks in each LOD column (format="allpheno");
or have one row per chrosome, containing the the position and LOD
score for each the peak from each LOD column (format="allpeaks").
The function now also can take permutation results in order to
automatically calculate LOD thresholds or to calculate
genome-scan-adjusted p-values.
- summary.scantwo: This was quite radically changed. For each pair of
chromosomes (including a chromosome with itself), we calculate five
LOD scores: the maximum LOD for the full model (2 QTL +
interaction), the maximum LOD for the additive model, the difference
between these (which concerns a test of whether the two loci
interact), and two LOD scores concerning 2 vs 1 QTL: the difference
between the full LOD and the best single-QTL LOD for the pair of
chromosomes, and the difference between the additive LOD and the
best single-QTL LOD for the pair of chromosomes. This is the
recommended output, indicated via the argument what="best". One may
also set the 'what' argument to "full", "add", or "int". (See the
help file for summary.scantwo.) The 'thresholds' argument now
requires five values, or one may provide permutation results plus a
set of five 'alphas' (significance levels). There is also an
argument 'allpairs'; the default is TRUE, in which case all pairs of
chromosomes are considered. If allpairs=FALSE, only the self-self
chromosomes are considered, so that one may look more easily for
cases of possible linked QTL.
- summary.scanone and max.scanone now can just just one object, rather
than multiple such, as before. However, we have added functions
c.scanone and cbind.scanoneperm for combining the columns in
multiple runs of scanone (generally either multiple phenotypes or
multiple methods).
- Completely revised the summary.scantwo function. The old version is
saved as the function summary.scantwo.old().
- Added an argument perm.strata to scanone and scantwo, to allow
stratified permutation tests. If provided, it should be a vector
of length the number of individuals in the cross; unique values in
perm.strata will specify the strata in which the permutations should
be performed. (For example, this could be an indicator of the sexes
of the individuals, in which case the individuals will be shuffled
separately within males and within females.)
- Permutations in scanone can now be done to give separate thresholds
for the autosomes and the X chromosome. The argument perm.Xsp is
used to indicate that this should be done, in which case many more
permutations will be run for the X chromosome than for the
autosomes, to ensure similar accuracy. The output of scanone when
n.perm>0 is now given class "scanoneperm", and we've written a
function summary.scanoneperm for getting LOD thresholds. (This is
necessary, since the calculation autosome- and X-chromosome-specific
thresholds is a bit complicated.) We've also added a function
c.scanoneperm for combining the results of multiple permutation
runs. (This because their combination is not so simple as before.)
- Added functions -.scanoneperm, +.scanoneperm, -.scantwoperm, and
+.scantwoperm, for taking sums or differences of permutation results
from scanone or scantwo. This is particularly useful for getting
LOD thresholds for QTL x covariate interactions, though one must be
careful to ensure that the permutations are perfectly linked, which
can be achieved with set.seed.
- The permutation results from scantwo are completely changed. Rather
than keep track of the maximum LOD score for the full model (two
QTLs + interaction) and the interaction LOD score, we keep track the
genome-wide maxima of the 5 LOD scores calculated in
summary.scantwo. (See above.) The output is now given a class
scantwoperm, and there is a summary.scantwoperm function for
calculating LOD thresholds. There is also a c.scantwoperm function
for combining results from multiple runs, largely for the case that
multiple sets of permutations were run in parallel.
- Removed the ability, in scanone and scantwo, to use the snow package
to do parallel analysis on a linux cluster. With the new changes in
scanone, I found the code to be too cumbersome.
- Added the extended Haley-Knott method (see Feenstra et al., Genetics
173:2269-2282, 2006) to the scanone function. This is faster and
more robust than standard interval mapping, and is a better
approximation (but slower) than regular Haley-Knott regression.
- Revised the sim.cross() function so that, with a backcross, the
effect in the "model" argument is to be specified as the difference
between the average phenotypes for the heterozygotes and the
homozygotes. (Previously, it was 1/2 this, which is
different from the typical parameterization.)
- Added the ability, for a backcross, to estimate a genetic map under
the Stahl model for crossover interference (of which the chi-square
model is a special case). Also added a function, fitstahl, for
getting the maximum likelihood estimates in the Stahl model (or the
chi-square model); the genotyping error probability may be treated
as known or may also be estimated.
- Added an argument, "use", to scanone and scantwo, for indicating, in
the case that multiple phenotypes are to be run, whether only
individuals with complete data on all phenotypes
(use="complete.obs") or all individuals (use="all.obs") are to be
used.
- The degrees of freedom are added as attributes in the output from
scanone and scantwo, including the case of permutations.
### Minor changes:
- In read.cross, the symbol "#" is no longer treated as a comment
character by default. The default is to use comment.char=""; that
is, no symbol is treated as an indicator of comments. For the
comma-delimited file formats, one may have a character interpreted
as indicating comments using the comment.char argument.
- Fixed a bug for the new "batch mode" permutations in scanone and
scantwo with method="hk" or ="imp". The trick only works if there
is no X chromosome or all individuals have the same sex and cross
direction or permutations are done stratified within sex and
direction.
- Added an argument "show.marker.names" to plot.map and plot.scanone,
so that marker names can be added to these plots.
- write.cross can now write data in the "csvr", "csvs" and "csvsr"
formats.
- Added a function plot.pheno for plotting a histogram or barplot of
a phenotype distribution.
- Added a function condense.scantwo for producing condensed versions
of scantwo output, containing just the maximum LOD scores on each
pair of chromosomes. One can get summaries from these but not
plots.
- In plot.info, added step, off.end, error.prob and map.function
arguments. The function now always calls calc.genoprob rather than
relying on the values in the data.
- Changed the default cutoff for genotyping error LOD scores in
top.errorlod and plot.geno to 4.
- Changed the name of the function clean() to clean.cross() and made
a new function clean() that will dispactch a cross object to
clean.cross. Added a function clean.scantwo() for cleaning up the
output of scantwo: any values that are missing or are < 0 are
replaced by 0 and any LOD scores for pairs of loci that do not have
a marker between them are set to 0.
- The output of scantwo() now contains the original genetic map as an
attribute; this is needed for clean.scantwo().
- Slightly revised effectplot() so that if sim.geno hasn't been run,
it is run (with a single imputation) before the plot is created.
I also changed the names in the output, so that it is "Means" and
"SEs". Changed the examples in the help file for effectplot.
- Added an argument "lodcolumn" to max.scanone, so that it behaves
like summary.scanone.
- Added a function subset.scanone() for pulling out particular
chromosomes or LOD score columns from scanone output.
- Added a function find.pseudomarker() for identifying the name of a
pseudomarker that is closest to a specified position. This is
useful for the effectplot() function.
- In scanone and scantwo, there is now a warning printed when
individuals with missing phenotype are dropped. Also, a slightly
better error message is printed if addcovar or intcovar are not
numeric. Also added a warning message if addcovar or intcovar
appear to be over-specified (having columns that need to be
dropped).
- Fixed a slight problem in the column names from scanone() in the
case of multiple phenotypes; changed the convention for this. Now
the columns will just have the phenotype names.
- Fixed the help file for read.cross concerning the individual
identifiers and about which files are used for the csvs and csvsr
formats.
- Revised nmissing() so that if what="ind" and individual IDs are
included as a cross phenotype (named "id" or "ID"), these are used
as names in the output.
- Revised summary.cross() to include a check of whether the individual
IDs (in a phenotype named "id" or "ID") are unique. If they are
not, a warning is issued.
- Changed the "pheno" argument in plot.cross to "pheno.col", to be
more consistent with other functions.
- Changed the name of the argument "which" in plot.rf and nmissing to
"what".
- Added an argument "verbose" to the ripple function; if
verbose=FALSE, the function doesn't print anything. Also modified
print.summary.ripple so that it prints no more than 6 rows.
- Revised plot.missing so that if reorder=TRUE, the reordering of
individuals is done by the average of only the numeric phenotypes
(rather than all phenotypes, which gave an error).
- Fixed a slight bug in summary.cross() regarding duplicate marker names.
- Fixed a bug in scanone() that messed up the X chromosome label in
the case of method="imp" with multiple phenotypes.
- Fixed a bug in scanone() regarding method="mr-imp" with
permutations.
- Revised the listeria data set slightly; added an "alleles"
attribute, with alleles "C" and "B", as this was a cross between
BALB/cByJ and C57BL/6ByJ, and those strains were coded C and B in
the original paper. This takes advantage of a feature added in
version 1.03. Also added a phenotype "sex" that indicates all
individuals are female.
- Added a phenotype "sex" in the hyper data, indicating that all
individuals are male.
- Modified checkAlleles() so that it doesn't give an error if one
inputs data for only the X chromosome.
- Revised calc.errorlod() so that it won't give a warning if it has to
run calc.genoprob() because such probabilities aren't available. It
will still give a warning if it has to re-run calc.genoprob() with a
new error.prob value.
- Slight revision of plot.scanone() to include "Chromosome" as an
x-axis label if multiple chromosomes are plotted.
- Fixed a slight bug in plot.info for the case that results are only
at the marker positions.
- Changed the name of the "cols" argument in plot.pxg to "col". (This
argument was added in version 1.03.)
- Revised summary.cross so that if the "jittermap" warning is printed,
it's only printed once.
- Made a slight change to summary.map and print.summary.map, so that
"sexsp" is an attribute.
- A couple of changes were made to the write.cross.qtlcart():
round the map locations, make sure backcross code is correct, and
make sure RIL data is written as 0/2 rather than 0/1.
- Revised plot.info() so that if method="entropy" or
method="variance", only the column requested is returned.
(Previously, the other was also given, but with all 0's.)
- Fixed a bug in sim.cross for type="4way"; it would stop with an
error if QTLs were to be simulated.
- Fixed a bug in fill.geno for the case that a chromosome has just one
marker.
- Removed the function convert.cross(), which converted cross data
from the format used in R/qtl version < 0.65 to the current format.
This shouldn't be needed anymore.
- Fixed a bug in plot.pxg; the plot was messed up one requested an
autosomal marker and an X chromosome marker, but with the X
chromosome marker listed first.
## Version 1.03, 7/20/2006:
### Major changes:
- Fixed subset.cross() so that the attribitutes in the results of
calc.genoprob, calc.errorlod, sim.geno, and argmax.geno, don't get
lost on subsetting. This was important to ensure that the package
will conform to a change that will occur in the next release of R.
- Added a function checkAlleles() for identifying loci that might have
their alleles switched (in an intercross, if AA and BB are switched,
or in a backcross if AA and AB are switched). The X chromosome is
ignored. An internal function, checkrf() was removed; this was
previously called by est.rf() but wasn't well written.
- Added an argument, alleles, for read.cross(), which takes two
single-character allele labels that are included as an attribute in
the cross and will be used as labels throughout the program (for
example, in geno.table, effectplot and plot.pxg). This required
numerous small changes throughout the package.
- The maps used for the results from argmax.geno(), calc.genoprob()
and sim.geno() are now saved as an attribute on the data they
create (within the cross object) so that create.map() doesn't have
to be called repeatedly.
- Moved the code for simulating genotype data in sim.cross() into C,
to increase speed, and modified it so that one may simulate under
Frank Stahl's interference model (which includes the chi-square
model as a special case).
- If one includes a phenotype named "id" or "ID", this will be used in
top.errorlod(), plot.errorlod(), and plot.geno() as identifiers for
the individual.
### Minor changes:
- Added a warning in summary.cross() if there are multiple X
chromosomes; the summary now includes the names of the autosomes
and X chromosome (for diagnostic purposes).
- Revised plot.rf() so that, if the results of est.rf aren't
available, that function is run.
- Made a slight modification to the bayesint() function for getting
Bayes credible intervals from scanone() results.
- Added a "chr" argument to pull.geno() and pull.map(), so that you
can pull out the genotype data or map for a selected set of
chromosomes.
- Fixed a slight bug in locatemarker(), used by makeqtl().
- Added a function print.map() so that when you print a map, all of
the class stuff doesn't get in the way.
- Included an additional argument [stepwidth = c("fixed", "variable")]
in the internal create.map function, for Brian Yandell and the
R/bmqtl package. This argument was also added to calc.genoprob(),
sim.geno() and argmax.geno(). We also added a "stepwidth"
attribute to the bits that these functions produce.
- Added an argument, "lodcolumn", to the function max.scantwo, for
picking out a single phenotype in the case that the results concern
multiple phenotypes. As with summary.scantwo() and plot.scantwo(),
this function will only give the results for a single phenotype.
- Made a slight change regarding the sizes of the labels in
plot.pxg() and added an argument concerning colors.
- Fixed a bug in scanqtl() regarding the X chromosome.
- Revised plot.map() slightly so that one can use "main" as an
argument, to create a custom title (such as "").
- Fixed a bug in sim.map() regarding sex.sp=TRUE
## Version 1.02, 6/2/2006:
### Major changes:
- Modified scanone() and scantwo() so that they may analyze multiple
phenotypes simultaneously. This can greatly speed up the analyses
with Haley-Knott regression (method="hk") and imputation
(method="imp"). We can use this trick to speed up permutation
tests: create multiple permuted phenotypes and then analyze them all
at once.
- scanone() results no longer include parameter estimates (such as the
phenotypic averages for each genotype group and the residual SD).
The bookkeeping for this became too painful as we moved to allow
multiple phenotypes to be analyzed simultaneously. To get such
estimates, use fitqtl(). fitqtl() currently works only via the
imputation method, but we expect to soon implement multiple interval
mapping (MIM) and also Haley-Knott regression.
- scantwo() with method="em" now works for the X chromosome, including
with model="binary".
- Modified the "map10" dataset: a genetic map modeled after the mouse,
with markers having an approximately 10 cM spacing. We've revised
the chromosome lengths to match those in the Mouse Genome Database.
- Dropped support for intercrosses with sex-specific maps (class
"f2ss").
- Changed the meaning of the argument "lodcolumn" in scanone(). It now
should be an index starting at 1 rather than 3. I think this will
be more clear for the case of LOD scores from multiple phenotypes,
though perhaps it will be less clear.
- summary.scanone() now takes an argument "lodcolumn"; if a single
scanone output is given as input, it picks off peaks using those LOD
scores. (As with plot.scanone, this is indexed starting at 1.)
- Similarly, added a "lodcolumn" argument to plot.scantwo() and
summary.scantwo(), for the case that the scantwo results are for
multiple phenotypes; only results for a single phenotype are used by
these functions, and "lodcolumn" indicates which one.
### Minor changes:
- Modified summary.cross() to give a warning if there are markers at
precisely the same position. Added a function jittermap() to assist
in fixing this. Numerous functions run into problems if there are
markers on top of each other. Revised the hyper dataset so that it
doesn't have this problem.
- Switched the order of the arguments "model" and "method" in scantwo()
to match that for scanone().
- Fixed a slight bug in max.scanone() that led to an unnecessary
warning message.
- Fixed a slight bug in locate.xo(), used by plot.geno() to identify
the locations of crossovers.
- Made a slight revision to read.map.qtlcart(), so that chromosome
names are not required in the map file, and so that more informative
messages are displayed if marker or chromosome names are not found.
- Modified qtlversion(), which prints the installed version of the
package, to use library(help=qtl) rather than installed.packages().
This is a lot faster.
- Added, to summary.cross(), a check on whether multiple phenotypes
have the same name.
- Modified plot.cross() so that it will work if multiple phenotypes
have the same name (though that shouldn't happen).
- Fixed a bug in fitqtl() regarding the names of coefficients for
interactions between QTLs and covariates when get.ests=TRUE.
- Fixed a slight problem in read.cross.csv() and read.cross.csvs() so
they will read in 4-way cross data. You need to use genotypes=NULL.
- Modified c.cross() so that it can combined crosses typed at
different numbers of markers. The number of chromosomes must be the
same, and the genetic maps must be consistent.
- Modified plot.scanone() so that you can give it a "ylab" argument to
override the y-axis labels. Eliminated the "main" argument, as that
can be passed via "...".
- Modified the threshold for est.rf() to print warnings about possibly
switched genotype data.
- Fixed a slight typo in the help file for plot.scantwo().
- Fixed a bug in calc.pairprob() (used by scantwo) for RILs.
- Fixed a slight bug in scanone() for permutations; it dropped
covariates in permutation tests with model="binary".
- Fixed a slight bug in read.cross with format "csvs", for the
case that the argument genotypes=NULL.
- Fixed a slight bug in checkcovar() used by scanone() that arose when
there were missing values in the phenotype data.
- Added a utility function chrlen() for pulling out the lengths of all
of the chromosomes.
## Version 1.01, 10/25/2005:
### Major changes:
- Revised read.cross to include three additional data formats:
```
"csvr" The format "csv", but with rows and columns
interchanged. I call that a "rotated" version of the CSV
format, but it's really a transposed version.
"csvs" The format "csv", but with separate files for the
genotype and phenotype data. Note that the first column
in the phenotype data should specify the individuals'
IDs, and that there should be a column in the phenotype
data with precisely the same name, and the individuals
should be in precisely the same order.
"csvsr" The format "csvs", but with the genotype and phenotype
files rotated (really transposed).
```
- Added example files (of the listeria data) in these formats in the
"sampledata" directory.
### Minor changes:
- plot.scantwo can now plot the additive LOD scores in the lower
triangle (with the argument lower="add")
- Fixed a bug regarding the X chromosome in scanone() with the use of
covariates.
- Modifying plot.geno() to put X's at inferred crossover locations.
- Modified plot.rf() so that the lines between chromosomes are white.
- Added a "chr" argument to plot.map, so that a selected set of
chromosomes may be plotted.
- Changed the default value for the error.prob argument from 0 to
0.0001 in est.map(), calc.genoprob(), sim.geno(), and other
functions.
## Version 1.00, 9/10/2005:
### Major changes:
- Revised fitqtl() so that it can provide estimated QTL effects (using
the imputation method), though this is working completely only for
autosomes in backcrosses and intercrosses at this point.
- Revised fitqtl() so that it treats the X chromosome appropriately.
### Minor changes:
- Fixed a bug in read.cross for the "qtlcart" format. There was a
problem in the reading of map files if the inter-marker distances
were at all out of alignment (which occurred when two markers were
100 cM apart).
- est.rf() was revised to treat the X chromosome properly in an
intercross.
- Fixed a bug in scanqtl() in the case that covar=NULL was specified;
this should be treated just like if it were missing.
- Modified plot.scantwo() so that the default is lower="joint"; I've
become suspicious of lower="cond-int" and "cond-add".
- Added another argument to plot.scantwo(): point.at.max, for plotting
an X at the maximum LOD.
- Added an argument, "verbose", to scanqtl(), to give feedback about
progress.
- Revised scanqtl() so that makeqtl() doesn't get called repeatedly,
but rather the imputations get copied over. This sped the thing up
immensely.
- Replaced calls to print.matrix() in print.summary.ripple(), as the
function will be dropped from R ver 2.2.
- Fixed a bug in plot.pxg(): it halted with an error in the case of
multiple markers on the same chromosome.
- Fixed a bug in fitqtl() that made it die with only one QTL.
- plot.scantwo() now gives cM locations on the axes in the case of
just one chromosome.
- Fixed a bug in find.marker.
- Fixed a slight bug in plot.scanone()
- Added a function qtlversion() to print the version number of the
currently installed version of the package.
- Fixed a bug in plot.scantwo() regarding the X chromosome in the case
that markers were included in scan but are not to be plotted.
- Fixed a bug in scanone() and scantwo() regarding the use of sex
and/or pgm as covariates on the X chromosome; this affected only
results with method="imp" and only for the X chromosome.
- Revised some of the help files so that they conform to the rules for
the latest version of R.
- Revised scantwo() by imputation so that the interaction LOD score is
obtained by combining across imputations for each of the full and
additive model and then subtracting, rather than subtracting and
then combining.
- Fixed some typos in the help files.
## Version 0.99, 4/26/2005:
### Major changes:
- scanone() now allows additive and interactive covariates in the
case model="binary" (that is, for a binary trait). This uses
a logit link.
- scantwo() now allows analysis of binary traits (model="binary"),
for method="em" only.
- Added a few new utility functions: bayesint() for calculating
Bayesian probability intervals [cf lodint()], comparegeno for
comparing individuals' genotypes, and strip.partials()
for removing partially informative genotypes.
- Added +.scanone() and -.scanone() for adding and subtracting the
output of scanone()
- Revised summary.scanone() and print.summary.scanone() so that it can
summarize the result of multiple scanone() results together.
- Added code (the function sim.cc) for simulating the "Collaborative
Cross" (8-way RILs) and for calculating QTL genotype probabilities
and identifying the most likely genotypes (using Viterbi) with SNP
data on such lines.
### Minor changes:
- Revised plot.scanone() so that when one chromosome is plotted, it
starts whereever the first marker on the chromosome was placed, and
not necessarily at 0.
- Revised plot.map() so that shifting chromosomes so that the first
marker is at 0 cM is optional. (Use shift=FALSE to not do such a
shift.)
- Fixed the issue regarding use of sex and/or pgm as covariates for
the X chromosome; such covariates are dropped just for the X
chromosome.
- Revised plot.pxg() so that it no longer returns Rsq, fit and so
forth. I've gone back to returning just information about the data
that are plotted. I added an argument "main" in the case one wishes
to use a plot title different from the default.
- Changed the default for plot.geno from horizontal=FALSE to
horizontal=TRUE.
- switch.order() no longer resets the location of the first marker on
the chromosome to 0 cM, but retains the offset from the original
map.
- Changed "trace" as an argument to "verbose", to avoid clashes with
the built-in R function trace()
- Revised summary.cross() to check the class of chromosomes (the
components in cross$geno); they should each have class "A" or "X".
- Revised subset.cross() so that it won't produce duplicate
chromosomes, and to treat missing values in the ind argument.
- Fixed a slight bug in fitqtl() regarding the drop one analysis
when there is just one QTL.
- There was a slight bug in plot.pxg() regarding the X chromosome.
- Fixed a bug in scanone() regarding the X chromosome for RILs.
- Fixed a slight, silly bug in est.map() for sex-specific maps, in
which the location of the initial marker was randomized.
- Revised plot.scanone(), plot.scantwo(), and other plotting functions
so that they don't show their NULL return values.
- Fixed a bug in makeqtl() regarding the X chromosome if there are
genotype probabilities.
- Revised the internal checkcovar() function to check that the chosen
phenotype for scanone(), scantwo(), etc., is numeric. Previously,
an rather uninformative error message was given.
- Modified the convergence criterion for scantwo() by the EM
algorithm; we now just look at the log likelihood, and not at the
parameters.
- Fixed a bug in read.map.qtlcart().
- Fixed bugs in scanone and scantwo for method="imp", for the case
that one has exactly one imputation. Fixed a memory-overwrite
problem in scanone() with method="imp".
- Fixed a bug in fixXgeno.f2; a slight error that shows up in the case
the pgm values are switched.
- Added code to simulate Collaborative Cross data and to do
calc.genoprob() and argmax.geno() on such data, though none of this
is documented yet.
- movemarker() now updates the results of est.rf, calc.genoprob,
calc.errorlod, sim.geno, argmax.geno, if they are available.
(est.rf is simply re-run; the others are re-run for just the
relevant chromosomes).
- calc.errorlod had neglected to include the map function as an
attribute. This is now fixed.
- Revised scantwo with method="em" so that it prints the verbose
warning messages only if the verbose argument is > 1. With
verbose=TRUE, only the chromosomes are printed.
## Version 0.98, 9/11/2004:
### Major changes:
- There is no longer an argument "sep" for the function read.cross.
Instead, we use "...", which is passed to the function read.table
(all this just for the "csv" format). (sep="," is still assumed for
that format). This change allows one to use sep=";" and dec=","
which many people prefer.
- The function read.cross now automatically converts X chromosome
genotype data into the standard internal format (with all
individuals coded like an autosome in a backcross).
- The functions scanone() and scantwo() were revised so that they
treat the X chromosome appropriately. The argument "x.treatment"
has been deleted. What had been x.treatment="full" (namely, that
hemizygous genotypes are considered different from homozygous
genotypes) is now forced. The big change concerns the "null
hypothesis" for the X chromosome, which includes sex and/or "pgm" as
covariates, in order to avoid spurious linkage on the X due to sex
differences in the phenotype. See the help files for these
functions for details. Note that the output of the scantwo function
has changed somewhat; it would be best to re-run scantwo with this
new version of the software.
- Added a function movemarker() for moving a marker from one
chromosome to another.
- Revised scanone(), scantwo(), discan(), vbscan() and plot.info() so
that inter-marker positions are cited as "c*.loc*" rather than
"loc*.c*" or "loc*". Added a function convert.scanone() for
converting scanone output to the new format. (The new plot.scantwo
will interpret, for the old version of scanone output, every
inter-marker position as a marker.)
### Minor changes:
- Added a function find.pheno() [from Brian Yandell] for finding the
phenotype column with a particular name.
- Added a function find.flanking() [from Brian Yandell], which is
similar to find.marker(), but gives not just the closest marker
but also the left- and right-flanking markers.
- Added a function print.cross() which prints a short message and then
calls summary.cross(). This was added in order to avoid the
essentially always unintentional printing of an entire (generally
quite large) cross object.
- Modified summary.scantwo to allow a type option to get summaries
based on peak "joint" or "inter" and to allow negative thresholds
relative to max joint, inter, or individual LODs [from Brian
Yandell; I'm not really sure what this means].
- Modified plot.scantwo to modify the contour option, making 1.5 from
the peak the default on each half-image, and to take a numeric
vector of drops from the peaks. Added arguments col.scheme and
gamma for different color schemes [from Brian Yandell].
- Hugely sped up plot.scantwo for the case of lower="cond-int" and
lower="cond-add"! (By hugely, I mean by a factor of 50 or more.)
- Added a function summary.map() for giving summary information about
a genetic map.
- In read.cross, if chromosome names start with "chr" or "chromosome"
(ignoring case) these initial strings are removed.
- est.rf now returns a warning if a marker appears to have its
genotypes miscoded (so that it shows a rec. frac. > 0.5 with
LOD > 3).
- Deleted the function pull.chr(), which was deprecated in version
0.89 in Nov, 2001. You can use subset.cross() instead.
- Fixed a bug in calc.errorlod regarding the X chromosome in an
intercross.
- read.cross with format="qtlcart" printed on screen the number of
individuals but called it the number of phenotypes. Brian Yandell
provided another revision to this, to fix bugs regarding phenotypes
that are factors.
- Fixed a slight bug in summary.cross() in the case that a cross
contains no autosomal data.
- Fixed a bug in read.cross for the mapmaker format; if a marker or
phenotype name were listed without any data, an error resulted.
- Fixed a bug in summary.scanone which resulted in multiple rows being
returned for a single chromosome if multiple positions shared the
same maximal LOD score.
- Fixed bugs in plot.scanone and plot.scantwo for the case that the
"chr" argument was used with chromosomes not in the usual order.
- read.cross with format="csv" now prints a warning if unusual entries
are seen in the genotype data.
- Revised the geno.table() function so that its first column is the
chromosome number
- Modified read.cross.qtx(); "X" or "x" in a phenotype is a missing
value.
- Changed a call to print.coefmat() to a call to printCoefmat(), as
the former is being discarded in favor of the latter.
- Changed the name of the utility function fixXdata() to
reviseXdata(). This function deals with the X chromosome genotypes
in scanone() and scantwo().
- Modified the source code in hmm_bc.c, hmm_f2.c, hmm_main.h so that
we don't repeatedly calculate log(0.5), log(2.0) and log(0.25), but
rather rely on #define statements
- Got rid of the WIN32 stuff in addlog and subtractlog in util.c,
which were used in version 0.97 as I'd not been able to get log1p to
work.
- plot.missing now gives a more meaningful error if the argument
"reorder" is greater than the number of phenotypes.
- I split up the read.cross.R file into several smaller files, for
more easy revisions.
- Revised the function comparecrosses(), adding an argument "tol" so
that the genetic maps and phenotypes do not need to be *exactly* the
same, but can be identical to within the specified tolerance, "tol".
Also, a warning (rather than an error) is produced if the
inter-marker distances are the same but the position of the initial
marker is different.
- Fixed a slight bug in write.cross for the case of phenotypes that
are factors.
- Fixed a problem in read.cross for format "gary"; now I pass the
"na.strings" argument for reading the phenotype data.
- Fixed a problem in read.cross with format "gary" or "csv" for
ensuring that phenotypes that appear to be numeric are read as
numeric and not as factors.
- Modified the function getsex(), which finds and interprets the sex
and pgm columns in the phenotype data, for the case where sex is
read as a factor with just one level (either "F", "f", "M", or "m").
- Added more understandable warning/error messages to plot.scanone if
a chromosome ID in the "chr" argument doesn't match those in the
scanone output.
- Fixed a problem in the example data "badorder"; chromosomes 2 and 3
were switched.
- Fixed a bug in read.cross for the QTL Cartographer format for the
case that there is just one individual.
- Modified some of the C calls to FORTRAN subroutines, using the
macro F77_CALL(), as this is recommended in the R documentation.
(Fortran routines currently used: dqrls, dpoco, dposl)
- Modified est.map so that it removes individuals with fewer than two
typed markers. Their presence is of no value in estimating the map,
and can really slow things down.
- Revised a number of the help files to make the automated tests of
the integrity of the software much faster.
- Revised read.cross.mm() so that (a) the cross type is taken as the
4th word (rather than the last word) on the first line, in case
someone includes additional characters, and (b) if the sample map
format is used but chromosome assignments are not provided, a
meaningful error message is displayed.
- Made a few very minor revisions to the "rqtltour.pdf" tutorial.
- Revised getgenonames() and reviseXdata() to remove the x.treatment
argument, which is now assumed to be "full". Revised effectplot()
and plot.pxg() accordingly.
- Modified the utility function to do map expansion in RIs for the X
chromosome. Need to modify things further to take account of the
lack of balance on the X chromosome...it's quite different from a
backcross.
- Revised plot.pxg() so that it can take a vector of marker names
[from Brian Yandell].
- Revised plot.scantwo to allow different color schemes and to give
contours at 1.5 (or other specified values) below the maximum LOD
[from Brian Yandell].
- Revised summary.scanone and print.summary.scanone so that
summary.scanone will never print anything, but will leave it to
print.summary.scanone to do so. (Previously, summary.scanone
printed a message if there were no peaks above the LOD threshold.)
summary.scantwo and print.summary.scantwo were revised similarly.
- Modified plot.scanone to allow NAs in the LOD scores.
- Revised scanone and scantwo so that n.perm=0 is treated the same as
if it were not provided.
- Fixed a bug in plot.rf() in the case that chromosomes are provided
out of order, in which case the thing plotted garbage. The fix
involved revising subset.cross() so that the chr argument is sorted.
- Replaced the example data sets with compressed versions.
- Had to modify part of the C code for scanone with model="2part".
I'd hard-coded some of the array limits!
- Changed the default line types and colors in plot.scanone().
- Added a warning for scanone() and scantwo() about the number of
individuals that are omitted due to missing phenotype or covariate
information.
- Revised write.cross so that X chromosome data is converted back
from our internal format to the standard format.
## Version 0.97, 6/19/2003:
### Major changes:
- Added an argument "weights" to the functions scanone and scantwo, to
allow differential weighting of individuals in a genome scan; these
are only used with model="normal".
- Modified the function "plot.scantwo" for plotting the results from a
two-dimensional, two-QTL genome scan. There are two new arguments:
lower controls what LOD scores are plot in the lower triangle
(lower="joint" corresponds to the previous version of this
function), while nodiag controls whether to plot the scanone results
on the diagonal. Using lower="cond-int" (the default) gets rid of
the "coattail" effect often seen when plotting the joint LOD
scores. Ted Lystig for suggested this modification.
- Added a new function effectscan() for plotting the estimated allelic
affect at all markers on selected chromosomes.
### Minor changes:
- Modified write.cross so that it will output data in "gary" format.
- Added a function lodint, for calculating LOD support intervals based
on results from scanone.
- Added a function nmissing(), which calculates the total number of
missing genotypes for each individual in a cross, or for each
marker.
- Added a function pull.geno() for pulling out the set of genotype
data for a cross as a single big matrix.
- Added a function comparecrosses() for verifying that two objects of
class "cross" are identical.
- The results of geno.table() now includes P-values from chi-square
tests for Mendelian segregation.
- Modified the function c.cross for combining crosses. You can now
combine backcrosses and intercrosses, provided that they have
exactly the same genetic maps. Further, we no longer discard the
results of sim.geno and calc.genoprob, provided that the same step,
off.end, and error.prob arguments were used.
- Added an additional argument, cex, to the function plot.geno, for
control of the size of the points in the plot. Also changed the
orientation of the plot when horiz=FALSE, so that the centromere is
at the top of the figure rather than the bottom.
- Fixed calc.pairprob so that it will work for RI lines ("risib" or
"riself"). Thus, scantwo should work with RI lines now.
- Updated read.cross for format="gary" so that the marker positions
file ("mapfile") and phenotype names file ("pnamesfile") are not
necessary. Set these arguments to NULL (e.g., mapfile=NULL) if the
corresponding files are not available.
- Added a "chr" argument to max.scanone, so you can get the maximum
LOD score for a particular chromosome.
- Revised the function switch.order() so that, if estimated
recombination fractions are present (i.e., est.rf() was used), these
are revised appropriately; previously they had been removed.
Also added err and map.function arguments, to be passed to est.map()
when the map is re-estimated.
- Revised scanone() and scantwo() slightly; the statement for
producing a warning regarding the use of method=="im" (vs "imp" or
"em") was slightly wrong.
- Fixed a slight bug in scanqtl() for the case that a fixed position
is provided rather than a range (commented out two lines).
- summary.cross() now prints a warning if $data objects are data
frames. (They should be simple matrices.)
- summary.cross() now prints a warning message if the genetic maps are
not matrices with 2 rows for "f2ss" and "4way" crosses, or are
matrices for other crosses.
- drop.markers() now prints a warning if some markers were not found.
- Added arguments ylim and add.legend to the function effectplot().
- Added arguments xlim and mtick to function plot.scanone(). (mtick
allows marker locations to be indicated by triangles rather than
line segments.)
- Fixed a bug in read.cross for the case that phenotypes have values
like "1x2".
- Fixed a slight bug in write.cross for the qtlcart format.
- Fixed a bug in read.cross for the qtlcart format regarding the
determination of whether a chromosome is autosomal or the X.
(Previously, looked for an "X" or "x" in the marker names; now look
at whether the chromosome names contains an "X" or "x".)
- Fixed a bug in makeqtl() for the case of a four-way cross. (Hadn't
dealt properly with sex-specific maps.
- fitqtl() now stops with a more meaningful error message if imputed
genotypes are not available in the input "qtl" object.
- Revised the marker names for the X chromosome in the map10 dataset
that is included.
- Revised est.map() for the case of a sex-specific f2 (cross type
"f2ss"); the starting map for the EM algorithm is randomized a bit.
- Revised a bunch of the R code files so that paste() is not included
within stop() or warn().
- In a couple of utility functions for the hidden Markov model engine,
I need access to the log1p() function, but I'm having trouble with
that in Windows. Thus, in Windows only, I use log(1+x) in place of
the preferred log1p() function.
- Added tests of input/output that are run when doing a check of the
package.
## Version 0.96, 9/13/2002:
### Major changes:
- None.
### Minor changes:
- Added Listeria data in QTL Cartographer format to the sampledata
directory.
- Revised read.cross and write.cross for QTL Cartographer format, so
that the cross types are converted between those of R/qtl ("f2",
"bc", "riself", "risib") and those of QTL Cartographer ("RI0",
"RI1", "RI2", "B1", "B2", "SF2", "RF2").
- Revised read.cross for the Mapmaker format. The map file can now be
in a second format, ".maps", which is created by Mapmaker/exp. The
function determines whether it has been presented with the .maps
format or the 2- or 3-column tabular format that has been
available. Brian Yandell wrote the function to read ".maps" files.
- Fixed a small bug in write.cross for the Mapmaker format, and
modified the ".prep" file that is created, so that marker distances
are no longer included, and including lines "framework chr*".
- Revised read.cross with format="csv", so that it gives more clear
error messages in some cases.
- Updated the R/qtl tutorial, rqtltour.pdf. This is now in a
directory "docs" in the R/qtl distribution.
## Version 0.95, 8/1/2002:
### Major changes:
- Modified the functions scanone and scantwo in order to treat the X
chromosome appropriately. Each has a new argument, x.treatment,
which indicates how to treat the X chromosome (in particular,
whether hemizygous males should be treated the same as homozygous
females). For analysis to proceed properly, there should be
columns "sex" and "pgm" in the phenotype data, indicating the sex
of each individual, and the direction of the cross. See the X
chromosome section of the help file for read.cross for more
information.
- Added another argument to plot.scanone, "lodcolumn", an integer (or
a vector of 3 integers) indicating which columns of the scanone
output should be plotted (generally column 3).
- Added two functions for plotting phenotypes against marker
genotypes. plot.pxg() plots the phenotypes against the genotypes
at a single marker. effectplot() plots the average phenotypes
against genotypes at one or two markers (or covariates). Also
added a function find.marker() which returns the name of the marker
closest to a specified position.
- Added facilities for analyzing recombinant inbred lines. We now
allow two additional cross types, "riself" (RI lines from selfing)
and "risib" (RI lines from sibling matings). Added an internal
function expand.rf.ri and made important modifications to
calc.genoprob, sim.geno, argmax.geno, and est.map. Also modified
summary.cross, print.summary.cross, geno.table, replace.map,
discan, ripple, scanone, scantwo, makeqtl, calc.errorlod, est.rf,
write.cross.mm, write.cross.csv.
- Replaced the example fake.f2 with some new data, which includes
both males and females and both directions of the intercross, in
order to illustrate the proper analysis of the X chromosome.
- Modified read.cross and write.cross (and added code from Brian
Yandell) to read and write data in QTL Cartographer format.
### Minor changes:
- Fixed a bug in read.cross; the "genotypes" argument needs to have
"C" and "D" reversed. "C" = "not BB" = 5 internally; "D" = "not AA"
= 4 internally. Thanks to Martin Grandona for identifying the
problem.
- Fixed a bug in read.cross for format "csv": an error occurred if
marker positions were not given and the first individual was
missing a phenotype. Thanks to Justin Borevitz and Norman
Warthmann for identifying the problem.
- Fixed a bug in fitqtl. Also added type III sums of squares table
and also nominal P-values.
- Revised the read.cross functions so that if the X chromosome data
is coded as A:B, it gets re-coded appropriately.
- Revised read.cross.mm and read.cross.csv so that if marker
positions are included, marker order is taken according to those
positions. (Previously, read.cross stopped with an error.)
- Added some additional example data, bristle3 and bristleX, from
Long et al. (1995) Genetics 139:1273-1291.
- Added an example genetic map, map10, containing 19 autosomes and an
X chromosome, with chromosome lengths approximately as in the
mouse and markers at approximately 10 cM spacing.
- Changed web references "biosun01.biostat.jhsph.edu" to
"www.biostat.jhsph.edu".
- Revised summary.cross to print an error if the cross type is not
one of "f2", "f2ss", "bc", "4way", "risib", or "riself".
- Revised plot.map so that, when genetic maps are plotted vertically,
the 1st marker is at the top (rather than at the bottom).
## Version 0.94, 5/30/2002:
### Major changes:
- Modified scanone and scantwo to include the methods "mr-imp" and
"mr-argmax", for performing "marker regression" by first filling
in any missing genotypes by one imputation ("mr-imp") or using the
Viterbi algorithm ("mr-argmax").
- Edited functions read.cross.*, argmax.geno, sim.cross, and
sim.draws, so that the data, argmax and draws portion of a cross
object are stored as integers. This can save considerable space.
- Added functions to perform a general scan by imputation:
fitqtl(), makeqtl(), scanqtl().
### Minor changes:
- Edited the read.cross.* functions again; now by default dir = ""
rather than ".", and I no longer remove any trailing "/" from dir.
- Added checks of genotype values in the function summary.cross.
- Rather than edit the read.cross function to read in X chromosome
data appropriately, I instead edited its help file, to explain that
X-linked data should be coded as an autosome in a backcross (with
genotypes A and H).
- Fixed slight errors in the functions scanone, calc.genoprob,
discan, calc.pairprob, and sim.geno regarding the naming of the
genotypes for the 4-way cross.
- Changed a couple of apostrophes to double-quotes in the function
summary.scantwo.
- Added a Morgan map function (mf.m and imf.m), with revisions to
argmax.geno, calc.genoprob, calc.pairprob, calc.errorlod, est.map,
ripple, sim.geno, sim.cross, sim.cross.bc, sim.cross.f2,
sim.cross.4way, fill.geno.
- Fixed a slight bug in ripple regarding the estimated chromosome
lengths in the case of a 4-way cross; I was picking out the wrong
element of the map.
- Fixed a bug in plot.scantwo regarding chromosome labels.
- Fixed bugs in max.scantwo and scantwo.perm regarding infinite LOD
scores (which comes up especially when running scantwo with
method="mr").
- Fixed a bug in read.cross.qtx regarding the determination of
whether a cross is a backcross or an intercross. Also fixed the
case of a backcross coded as H:B rather than A:H.
- Added a warning in summary.cross regarding duplicate markers.
- Modified the example cross data (such as hyper and listeria) so
that genotypes are stored as integers.
- Updated the "README.txt" file, to include explanations for
installation of R and R/qtl on Mac OS.
- Changed the default for the na.strings argument in read.cross and
read.cross.csv to include "NA".
- Changed a couple of lines in write.cross.csv and write.cross.mm for
the treatment of NA strings.
- Modified ripple so that orders considered are printed in a way that
the left-most marker in the original order is always to the left
of the right-most marker in the original order.
- In various functions, made sure that 0 < error.prob < 1.
- Edited plot.scanone so that when only one chromosome is plotted,
the chromosome number doesn't appear at the top, and when multiple
chromosomes are plotted, the chromosome numbers appear at the
bottom, rather than cumulative cM position.
- Changed the addcov and intcov arguments to scanone and scantwo to
addcovar and intcovar, respectively.
## Version 0.93, 4/1/2002:
### Major changes:
- Added ability to read data in Mapmanager QTX format. This may be
done via the read.cross function by using the argument
format="qtx". Added a file in this format to the sampledata
directory distributed with R/qtl.
- Modified function ripple(), which compares marker orders, so that
it may evaluate counts of obligate crossovers, which will be
extremely quick relative to performing an exact likelihood
calculation. This method has been made the default.
### Minor changes:
- Added functions max.scanone and max.scantwo for getting information
on the location with the highest LOD or joint and interaction LODs
- Modified summary.scantwo so that if the argument thresholds has
length 1, the interaction and conditional thresholds are assumed to
be 0 (so that all chromosome pairs for which the maximum joint LOD
is greater than the given threshold are printed).
- Revised the C functions emit_bc(), emit_f2(), emit_f2ss() and
emit_4way() so that unexpected observed genotypes are treated as
missing.
- Revised read.cross, read.cross.csv and read.cross.mm slightly, so
that estimate.map is TRUE by default, and so that the genetic maps
are re-estimated only if both estimate.map is TRUE and the genetic
map is missing from the input files. If estimate.map is FALSE and
the genetic map is missing from the input files, a dummy genetic
map is inserted.
- Fixed a bug in sim.cross, sorting the "model" matrix in advance of
performing the simulation, because the results were erroneous if
QTLs were specified out of order.
- Edited the functions read.cross.* to use the function file.path()
to create file names.
## Version 0.92, 2/12/2002:
### Minor changes:
- In read.cross.mm and read.cross.csv, when using the function
read.table, we replaced the use of as.is=TRUE with
colClasses="character". Apparently as.is=TRUE didn't work in R
version 1.4.0.
- In read.cross, changed the default of the argument "estimate.map"
to FALSE.
## Version 0.91, 12/3/2001:
### Minor changes:
- Fixed a problem with chromosome labels in plot.scantwo.
- Fixed a slight bug in summary.ripple.
- Previously forgot to implement the use of the "main" arg for
plot.scanone.
- Fixed a slight bug in read.cross.gary related to having just one
marker on a chromosome.
- Fixed a slight bug in plot.cross for the case auto.layout=FALSE.
- Revised read.cross so that, for the csv format, if the argument
"genotypes" is NULL, the genotypes are assumed to be correct. If
there are genotypes > 5, it is assumed to be a 4-way cross.
- For some reason, the wrapper for est_map for 4-way crosses got
deleted. I've re-written it. Hopefully it works!
- Fixed a slight bug in plot.map for plotting two sex-specific maps.
(The function works by pulling apart the sex-specific maps and then
calling plot.map again twice. After those calls, it should return.)
- Expanded examples in the help file for fake.4way.
- Fixed a bug in create.map for sex-specific maps.
- Revised calc.genoprob, argmax.geno and sim.geno so that, in the case
of one marker on a chromosome, off.end is forced to be > 0.
- Revised plot.scanone so that if there is exactly one LOD score for a
chromosome, a small segment is plotted rather than a dot.
- Fixed a couple of minor bugs in read.cross for the mapmaker format:
in dealing with the "symbols" information in the mapmaker file, and
in counting the number of lines in the file.
- Added a utility function checkcovar() to check phenotypes and
covariates in scanone and scantwo (thus removing some redundancy).
## Version 0.90, 11/24/2001:
### Minor changes:
- Replaced the example data fake.bc with something that will allow the
illustration of the use of covariates.
- Added print.summary.ripple; I'd forgotten to write it before.
- Added an updated tutorial on R/qtl, distributed as the file
rqtltour.pdf
## Version 0.89, 11/22/2001:
### Major changes:
- Consolidated scanone, vbscan and discan into the single function
scanone, with an argument model=c("normal","binary","2part","np").
The non-parametric "method" is now a "model".
- Buried scanone.perm and scantwo.perm as internal functions. To do
permutation tests, one now uses the main functions (such as scantwo)
and specifies the n.perm argument.
- Similarly, read.cross.* and write.cross.* were buried, so that the
user is expected to call either read.cross or write.cross rather
than calling the format-specific functions directly. This was done
anticipating an increase in the number of such format-specific
read.cross functions.
- Got rid of find.errors and plot.errors, as I don't like them. Use
calc.errorlod and plot.errorlod instead.
- Wanted to toss pull.chr, but instead just kept an internal version
which calls subset.cross and prints a warning, in case our one
official user has code which requires it.
### Minor changes:
- Added an "eq.spacing" argument to sim.map for generating maps with
equally-spaced markers. This seems more useful than putting them
down at random.
- Re-wrote a great deal of the help documentation (especially the
examples and details).
- Added a new example data set, badorder, with some errors in marker
order. (This is to illustrate the functions est.rf, ripple and
switch.order.)
- Fixed a slight error in summary.scantwo. We print pairs of loci
only if their joint LOD exceeds its threshold and either (a) the
epistasis LOD exceeds its threshold or (b) both conditional LODs
exceed their thresholds.
- Totally re-wrote print.summary.scantwo. It was unnecessarily
complicated before.
- Made a very slight change regarding the zlim in plot.scantwo.
- Fixed scantwo, summary.scantwo and plot.scantwo to deal with cases
of bad LOD scores (NAs, negative numbers and Infs). A warning
message will always be printed.
- Modified scanone_imp.c so that nullRss and altRss don't allocate
memory each time. Fixed a very bad bug in dealing with interactive
covariates. Fixed a single-character bug in scantwo_mr.c that was
causing a core dump.
## Version 0.88, 11/20/2001:
### Major changes:
- Added a scantwo function to do two-dimensional genome scans,
calculating LOD scores for a two-QTL model and to test epistasis
between each pair, with calculations done by imputation, Haley-Knott
regression, marker regression or the EM algorithm. Hao Wu wrote the
imputation method.
- With Hao Wu, wrote plot.scantwo to plot the results of scantwo,
summary.scantwo to summarize the results, and scantwo.perm to get
genome-wide LOD thresholds for a 2-dimensional genome scan by
permutation tests. The summary.scantwo function uses a criterion
due to Gary Churchill and Saunak Sen.
- Added a C function to calculate joint genotype probabilities for
pairs of putative QTLs on the same chromosome. Because the
resulting set of probabilities can take up a lot of memory, we're
not going to make these accessible to the user. The function
calc.pairprob was created, but this is not to be called by the user,
but rather will be called when needed.
### Minor changes:
- Added a "method" argument to vbscan, even though only method="em" is
currently available.
- Revised scanone, scantwo, discan, vbscan, and their corresponding
".perm" functions so that the output has attribute "method" to
indicate what method was used and attribute "type" to indicate the
type of cross that was analyzed.
- Changed method="im" to method="em" in scanone and discan; changed
method="markreg" again, this time to method="mg". Changed the order
of these methods in scanone.
- calc.genoprob now includes an attribute "map.function" with the
probabilities.
- Changed colors plotted in plot.rf.
- Modified the C function scanone_mr (marker regression) to avoid
repeatedly running the null model regression in the case of complete
marker data.
- Changed a good amount of R code like "1:length(x)" to "seq(along=x)"
- Added a function fill.geno for imputing missing marker data by
simulation (through sim.geno) or by the Viterbi algorithm (through
argmax.geno), so that one may perform quick-and-dirty (with an
emphasis on dirty) genome scans by marker regression.
- Fixed a small bug in sim.cross.f2.
- Fixed some problems related to chromosomes with only one marker:
read.cross.csv, create.map, subset.cross.
- Fixed a bug in the location of chromosome labels in plot.scanone.
Added an argument "main" for placing a title on the plot.
- Revised lots of little pieces of code using "drop=FALSE" when
subsetting a matrix or array in order to retain the structure.
- read.cross.csv can now deal with categorical phenotypes, and
plot.cross was revised to deal with such non-numeric phenotypes.
Added an argument "auto.layout"; if TRUE, mfrow is set so that the
many plots produced will all fit in one figure. par(ask=TRUE) is no
longer ever set.
- Revised sim.cross so that when keep.qtlgeno=TRUE, the QTL genotypes
are retained in a component cross$qtlgeno (rather than within the
data matrices).
## Version 0.87, 11/13/2001:
### Major changes:
- Hao Wu (hao@jax.org) has implemented the imputation method of Sen
and Churchill (2001) for a genome scan, included as method="imp" in
the function scanone.
- Added a non-parametric method to the function scanone, using a
modified version of the Kruskal-Wallis test (cf Kruglyak and Lander
1995).
- scanone now allows the use of covariates for all methods except the
non-parametric method.
- Phenotypes in a cross object are now a data.frame. Modified example
data files and the following functions to make this work:
sim.cross.*, read.cross.*, summary.cross, write.cross.csv.
### Minor changes:
- Changed the name of the "anova" method in scanone to "markreg".
- Changed the name of the argument "print.rf" in the est.map function
to "trace."
- Modified the default cutoff in top.errorlod; allow cuts and colors
in plot.errorlod to be specified by the user.
- summary.cross() now checks that markers are in increasing order.
- Made the third row (marker positions) in csv file optional in
read.cross.csv.
- Added a utility function subset.cross() for pulling out specified
chromosomes or groups of individuals from a cross object. We should
not need pull.chr() any longer.
- Added a utility function c.cross() for concatenating multiple cross
objects.
- Changed stopping rules for discan, discan.perm, vbscan, vbscan.perm,
est.map, est.rf, ripple, scanone, scanone.perm:
|x(s+1) - x(s)| < e {|x(s)| + e*100} where by default e = 1e-4
- Fixed the utility function create.map() for the case where the
genetic map starts at somewhere other than 0.
- Placed help information for discan.perm, scanone.perm and
vbscan.perm within the files for discan, scanone and vbscan,
respectively.
## Version 0.86, 11/4/2001:
- Fixed a *real* bug in argmax.geno().
- Added discan() for doing interval mapping with a dichotomous trait.
- Added documentation for the print.summary.* and internal functions.
- Edited documentation files to conform to R guidelines.
- Reduced the minimum value of the error.prob argument in est.map,
calc.genoprob, argmax.geno and sim.geno from 1e-14 to 1e-50.
## Version 0.85, 10/29/2001:
- Tried to fix up some of the plot.* and summary.* functions so that I
don't get warning messages in "R CMD check".
- Fixed a few minor problems in the help files.
- Updated the a.starting.point() help file.
- Fixed a couple of problems in marker order in the hyper data.
- Added plot.info() for plotting the proportion of missing information
in the genotype data.
- Fixed bug in plot.scanone() that led to problems in overlaying LOD
curves using add=TRUE. Added an argument, gap, to specify the
distance between chromosomes.
- Fixed bug in print.summary.scanone() that resulted in an error when
there was just one chromosome with LOD above the specified
threshold.
## Version 0.84, 10/10/2001:
- Fixed slight error in sim.cross(); marker genotypes were removed
rather than qtl genotypes. We now use the function drop.qtlgeno()
to do this.
- Changed anova method in scanone() to use observed genotypes.
Individuals with missing or partially missing genotypes are dropped.
- Added Haley-Knott regression method to scanone().
- Added a function ripple() for comparing marker orders for a single
chromosome, looking at all permutations of a sliding window of
markers. Also added switch.order() to switch the order of markers
on a specified chromosome.
- Removed null markers from listeria data.
- Fixed bugs in read.cross.mm() and write.cross.mm().
- Added csv and mapmaker format files to sample data directory.
- Allow specification of starting value is scanone and vbscan
- Added a document "rqtltour.pdf" describing the package and giving a
couple of examples.
## Version 0.83, 09/23/2001:
- Fixed a very slight bug in summary.scanone().
- Changed the argument "which.chr" in plot.scanone() to simply "chr".
- Added a "chr" argument to plot.missing().
## Version 0.82, 09/20/2001:
- Added write.cross.csv(), for writing data in comma-delimited format.
Changed write.mm() to write.cross.mm() and added write.cross() as a
wrapper to these two functions.
- All functions that use map functions now allow use of the
Carter-Falconer map function.
- Changed remove.markers(), remove.nullmarkers(), and remove.qtlgeno()
to drop.markers(), drop.nullmarkers() and drop.qtlgeno().
- Revised plot.rf() so that missing values appear in gray.
- Added read.cross.gary(), to read data in Gary's format, and
read.cross.csv(), to read data in comma-delimited format.
- Fixed the bugs in read.cross.mm(); see BUGS.txt.
- Fixed summary.cross() so that it checks marker names in the data and
the map.
- Added summary.scanone(), giving a summary of the output of
scanone().
- Added possibility of F2 intercross with sex-specific maps. Use
class "f2ss" rather than "f2." This is in the testing stage.
The only revised functions, at this point, are est.map() and
calc.genoprob().
- Added a function convert2ss() to convert a cross object from "f2"
to "f2ss" format.
## Version 0.81, 09/16/2001:
- plot.scanone can now plot three scanone outputs, and includes an
"add" argument for adding additional outputs to a current plot.
- Replaced 1e-10 with 1e-14 as tolerance value for error probability
and minimum map distance.
- Changed the "min.d" argument in plot.geno() to "min.sep", taken to
be a percent of the chromosome length.
- Added Carter-Falconer map function: mf.cf() and imf.cf(). Note that
there is no closed-form version of mf.cf(), and so I use the R
function uniroot().
- Fixed a slight error in replace.map().
- In est.map, calculate the log likelihood at the end; this is saved
as an attribute, "loglik" for each chromosome's map. If the "print"
argument is used, print the loglik, too.
- Made error.prob=0 the default for the functions argmax.geno(),
calc.genoprob(), est.map(), and sim.geno().
- Fixed the file permissions for many of the files, so that they are
readable by all users.
## Version 0.80, 08/07/2001:
- Eliminated the map component of the results of calc.genoprob,
argmax.geno, and sim.geno. Since we are now including attributes
"error.prob," "step," and "off.end," we can just use create.map() to
recreate the map each time, without having to carry it along.
- Changed the name of plot.geno() to plot.missing() and plot.chr() to
plot.geno().
- Added vbscan() and vbscan.perm() to perform the analysis described
in V Boyartchuk et al. (2001), for a phenotype where some
individuals have some quantitative phenotype, while for others it is
undefined. (Examples: the size of a lesion, where some individuals
exhibit no lesion; time-to-death after an infection, where some
individuals recover from the infection.)
## Version 0.79, 07/27/2001:
- Added map functions (and inversion map functions) for Haldane and
Kosambi, so that I'm not re-creating them all of the time within
functions.
- Added a function plot.chr() to plot genotypes for a specific
chromosome, with likely errors (as determined by calc.errorlod() or
find.errors()) highlighted.
- Added a warning to the help file for argmax.geno. The results
greatly depend on the value of the step argument, and may not be
terribly trustworthy. Also, if several sequences (of underlying
genotypes) are all most likely, our method of randomly choosing
among them is not right...recombination events are too far to the
right.
## Version 0.78, 07/24/2001:
- Fixed a small bug in create.map(), which is used by
calc.genoprob(). An error occurred in the case of a genetic
map with equally spaced markers, when the argument "step" was set to
be exactly the inter-marker distance.
- Modified calc.genoprob(), calc.argmax(), sim.geno() and
calc.errorlod() so that their corresponding components have
attributes "error.prob", "step" and "off.end" (only "error.prob" for
calc.errorlod()), specifying the corresponding values used in the
calculations. Modified calc.errorlod() to re-run calc.genoprob() if
the error.prob attribute is different from the corresponding
argument.
## Version 0.77, 06/22/2001:
- Fixed a small bug in sim.cross(), where dimnames of error component
was wrong, when simulating genotyping errors with a QTL present.
## Version 0.76, 05/17/2001:
- This is a totally revised version of the package. Most
importantly, the data structure for a cross has completely
changed. The function convert.cross is included, for converting
data from the old structure to the new one. See the help file for
read.cross for a description of the new data structure.
- The main hidden Markov model engine has been rewritten, to make
things more flexible and general. We've now implemented the Viterbi
algorithm, in the function argmax.geno, to calculate the most likely
sequence of underlying genotypes, given the observed marker data,
and we've fixed the calculation of the Lincoln and Lander error LOD
scores. The analysis of phase-known four-way crosses is now
possible.
- The "singlescan" function (to do a genome scan with a single QTL
model) is now called "scanone" (to save a few keystrokes). Note
that this function does not yet allow the use of covariates. We'll
add that feature in the near future.
- Saunak Sen and I are now working together on this project, and so
things will begin to progress more quickly (we hope).
