The pheno2geno package

Pheno2geno is an R package to create genetic maps out of phenotype expression data. Currently supported breeding schemes are: Recombinant Inbred Lines (RIL), F2 and backcross (BC). The master branch is the current stable version and is tagged. The master branch can be installed into R, development branches may contain errors.

Dependencies

• R software environment from www.r-project.org
• qtl package from www.rqtl.org

also available on CRAN

• mixtools package available on CRAN

Optional: RankProd package from www.bioconductor.org

Installation

The easiest way is to use package devtools. Type in R:

install.packages("devtools")
library(devtools)
install_github(repo="phenotypes2genotypes",username="KonradZych")
library("pheno2geno")

Starting

Load the library in the R interface by the following command (in R):

library(pheno2geno)

You can always access the help files of the package or for any function by typing:

?pheno2geno
?function.name

Or:

help(pheno2geno)
help(function.name)

To read in data files, use the read.population function:

population <- read.population(founders_groups=c(0,0,1,1))

In the help file of this function there is a description of the expected file formats. For more information see the manual.

TODO

See inst/TODO.txt

Contributing

Want to contribute? Great!

a) Clone a local version of the Github repository to your own hard disk:

git clone git://github.com/KonradZych/phenotypes2genotypes.git

b) Install it from the commandline by using the following command:

R CMD INSTALL phenotypes2genotypes

c) Then start R and load the library to make the functions available:

library(pheno2geno)

d) Modify some code. (Search -> 'TODO')

e) To check if the package is able to install in R:

R CMD check phenotypes2genotypes

f) If it's warning-free, go back to b) or submit a push request!

You can also just post comments on code / commits.

Disclaimer

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 3, as published by the Free Software Foundation.

This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License, version 3, for more details.

A copy of the GNU General Public License, version 3, is available at https://www.r-project.org/Licenses/GPL-3

Copyright (c) 2010-2012 GBIC - Danny Arends, Konrad Zych, Ritsert C. Jansen