Learn R Programming

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

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

Copy Link

Version

Install

install.packages('pheno2geno')

Monthly Downloads

70

Version

1.4.0

License

GPL-3

Maintainer

Last Published

February 11th, 2018

Functions in pheno2geno (1.4.0)

pheno2geno-package

Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes
reorganizeMarkersWithin

Reorganize markers within cross object.
save.gff

Saving gff files.
read.population

Loading genotype and phenotype data
testCross

Test cross object
markersCorPlot

Plotting correlation between markers on two maps.
qtl.comparison.plot

Comparison of qtl profiles.
pull.biomarkers

Extract the detected biomarkers from a population object.
testPopulation

Test population object
write.population

Writes a population object to file.
transformation

Basic functions to do transformation / normalization of phenotypes.
set.geno.from.cross

Pull genotype from an object of class cross.
projectOldMarkers

Plotting routine which shows where markers from original map are located on saturated map.
power.plot

Comparison of power of qtl detection.
scan.qtls

Scan qtls
fake.population

Simulate a population object.
cross.saturate

Saturate an existing genetic map.
create.population

Create a population object
find.mixups

Find sample mix-ups
cross.denovo

Create a de novo genetic map from a population object.
RPpval

Visualize the outcome of a Rank product analysis
modify number of chromosomes

Change the number of chromosomes in a cross object
find.diff.expressed

Finding differentially expressed genes.
assignChrToMarkers

Function that assigns a chromosome label to a genetic marker
add.to.population

Add additional data to a population object
generate.biomarkers

Generate discrete biomarkers from the continuous phenotypes
phenotypes2genotypes-internal

Internal pheno2geno functions
map.functions

Functions to provide some descriptive statistics on genetic maps
plotParentalExpression

Plotting routine for parental expression data.
markerPlacementPlot

Plot number of markers selected.
plotChildrenExpression

Plotting routine for children expression data.
plotMarkerDistribution

plotMarkerDistribution
plotMapComparison

Plotting routine for comparison of two genetic maps.