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synbreed (version 0.12-6)

Framework for the Analysis of Genomic Prediction Data using R

Description

A collection of functions required for genomic prediction which were developed within the Synbreed project for synergistic plant and animal breeding (). This covers data processing, data visualization, and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats in plant and animal breeding. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).

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Version

Install

install.packages('synbreed')

Monthly Downloads

26

Version

0.12-6

License

GPL-3

Maintainer

Hans-Juergen Auinger

Last Published

April 21st, 2017

Functions in synbreed (0.12-6)

pairwiseLD

LDDist

crossVal

Cross validation of different prediction models
discard.individuals

read.vcf2matrix

simul.pedigree

simul.phenotype

summary.LDdf

write.relationshipMatrix

write.vcf

[.GenMap

[.relationshipMatrix

plotGenMap

plot.pedigree

summary.gpMod

summaryGenMap

add.individuals

add.markers

discard.markers

gpData2cross

add.pedigree

Merge
codeGeno

create.gpData

create.pedigree

summary.pedigree

summary.relationshipMatrix

kin

manhattanPlot

plot.relationshipMatrix

write.beagle

write.plink

predict.gpMod

read.vcf2list

summary.cvData

summary.gpData

plotNeighbourLD

LDMap

MME

gpData2data.frame

gpMod

plot.LDdf

plot.LDmat