https://github.com/cran/ape
Tip revision: 604b6ae97eb19bae9675d37c9b1d864bcf77afe5 authored by Emmanuel Paradis on 27 May 2014, 00:00:00 UTC
version 3.1-2
version 3.1-2
Tip revision: 604b6ae
dist.gene.Rd
\name{dist.gene}
\alias{dist.gene}
\title{Pairwise Distances from Genetic Data}
\usage{
dist.gene(x, method = "pairwise", pairwise.deletion = FALSE,
variance = FALSE)
}
\arguments{
\item{x}{a matrix or a data frame (will be coerced as a matrix).}
\item{method}{a character string specifying the method used to compute
the distances; two choices are available: \code{"pairwise"} and
\code{"percentage"}, or any unambiguous abbreviation of these.}
\item{pairwise.deletion}{a logical indicating whether to delete the
columns with missing data on a pairwise basis. The default is to
delete the columns with at least one missing observation.}
\item{variance}{a logical, indicates whether the variance of the
distances should be returned (default to \code{FALSE}).}
}
\description{
This function computes a matrix of distances between pairs of
individuals from a matrix or a data frame of genetic data.
}
\details{
This function is meant to be very general and accepts different kinds
of data (alleles, haplotypes, SNP, DNA sequences, \dots). The rows of
the data matrix represent the individuals, and the columns the loci.
In the case of the pairwise method, the distance \eqn{d} between two
individuals is the number of loci for which they differ, and the
associated variance is \eqn{d(L - d)/L}, where \eqn{L} is the number
of loci.
In the case of the percentage method, this distance is divided by \eqn{L},
and the associated variance is \eqn{d(1 - d)/L}.
For more elaborate distances with DNA sequences, see the function
\code{dist.dna}.
}
\note{
Missing data (\code{NA}) are coded and treated in R's usual way.
}
\value{
an object of class \code{dist}. If \code{variance = TRUE} an
attribute called \code{"variance"} is given to the returned object.
}
\author{Emmanuel Paradis}
\seealso{
\code{\link{dist.dna}}, \code{\link{cophenetic.phylo}},
\code{\link[stats]{dist}}
}
\keyword{manip}