https://github.com/fchuffar/epimedtools
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README.md
# epimedtools
[![Build Status](https://api.travis-ci.org/fchuffar/epimedtools.png?branch=master)](https://travis-ci.org/fchuffar/epimedtools)
[![Coverage Status](https://img.shields.io/codecov/c/github/fchuffar/epimedtools/master.svg)](https://codecov.io/github/fchuffar/epimedtools?branch=master)
The __epimedtools__ package provides set of useful statistical functions. This package rely on 'GEOquery' and 'affy' packages, R Reference Classes, caching features and memoisation to simplify, homogenize and speed up multi-omic analysis.
## Data Structure
The __epimedtools__ package aims to manage a `study` object composed of the three data structure: the `data` matrix and the two `exp_grp` and `platform` dataframes.
Take care:
- study$data is a matrix of numerics
- `colnames(study$data)` contains `rownames(study$exp_grp)`
- `rownames(study$data)` contains `rownames(study$platform)`
```R
> study
#' $data
#' ctrl1 ctrl2 ctrl3 ctrl4 ctrl5 ctrl6 case1 case2 case3 case4 case5 case6
#' prb1 1.801 3.036 1.856 2.717 2.374 3.755 0.000 3.656 0.725 5.043 3.265 3.539
#' prb2 4.369 3.190 3.025 3.591 2.363 2.120 3.503 3.685 2.948 2.751 3.656 2.525
#' prb3 2.650 3.198 2.660 1.827 4.225 3.284 0.677 1.382 3.741 1.568 3.287 2.930
#' prb4 3.546 3.589 1.904 1.925 2.968 2.349 2.608 3.467 2.098 3.541 2.854 1.796
#' prb5 1.721 2.419 3.216 1.936 3.419 2.881 1.959 2.040 2.325 2.973 4.222 2.918
#' prb6 3.963 4.579 4.468 3.106 4.373 3.699 2.575 2.107 3.588 3.329 3.626 0.257
#' prb7 3.305 2.019 4.151 3.240 3.758 3.150 5.418 1.672 3.073 3.425 2.434 0.734
#' prb8 3.657 1.829 5.768 2.217 3.377 2.493 4.815 2.900 4.521 4.502 2.144 3.973
#' prb9 2.158 3.413 3.564 2.754 2.634 2.556 2.868 1.514 2.705 4.202 2.030 1.197
#' prb10 3.390 2.958 2.204 4.523 2.152 4.561 1.629 0.891 2.519 2.783 1.541 2.375
#'
#' $exp_grp
#' sex age tabac treatment histo
#' ctrl1 Female 23 Smoker 0 ug lung
#' ctrl2 Male 28 Smoker 0 ug lung
#' ctrl3 Female 26 Smoker 0 ug lung
#' ctrl4 Female 30 Non Smoker 0 ug lung
#' ctrl5 Male 22 Non Smoker 0 ug lung
#' ctrl6 Male 23 Non Smoker 0 ug lung
#' case1 Male 25 Smoker 15 ug lung
#' case2 Female 27 Smoker 15 ug lung
#' case3 Male 29 Smoker 15 ug lung
#' case4 Female 23 Non Smoker 15 ug lung
#' case5 Male 23 Non Smoker 15 ug lung
#' case6 Male 25 Non Smoker 15 ug lung
#'
#' $platform
#' GB_ACC Species Gene Symbol ENTREZ_GENE_ID
#' prb1 1U48705 Homo sapiens DDR1 780
#' prb2 2M87338 Homo sapiens RFC2 5982
#' prb3 3X51757 Homo sapiens HSPA6 3310
#' prb4 4X69699 Homo sapiens PAX8 7849
#' prb5 5L36861 Homo sapiens GUCA1A 2978
#' prb6 6L13852 Homo sapiens UBA7 7318
#' prb7 7X55005 Homo sapiens THRA 7067
#' prb8 8X79510 Homo sapiens PTPN21 11099
#' prb9 9M21121 Homo sapiens CCL5 6352
#' prb10 1J02843 Homo sapiens CYP2E1 1571
```
## Treatment and Analysis Features
The __epimedtools__ package provides not only a set of treatment features like data fetching or normalization, but also genome and genes anlysis tools.
## Installation
To get the current development version from github, you need first to install following packages from bioconductor:
* `Biobase`
* `affy`
* `GEOquery`
```R
# install.packages("BiocManager")
BiocManager::install(c("Biobase", "affy", "GEOquery"))
```
Then, install ``epimedtool``:
```R
# install.packages("devtools")
devtools::install_github("fchuffar/epimedtools")
```
## Vignettes
To browse available vignettes:
```R
browseVignettes(package = 'epimedtools')
```