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synbreed (version 0.9-3)

Framework for the analysis of genomic prediction data using R

Description

The package was developed within the Synbreed project for synergistic plant and animal breeding (www.synbreed.tum.de). It contains a collection of functions required for genomic prediction in both 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. 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

20

Version

0.9-3

License

GPL-2

Maintainer

Valentin Wimmer

Last Published

May 25th, 2012

Functions in synbreed (0.9-3)

[.relationshipMatrix

Extract or replace part of relationship matrix
LDMap

LD Heatmap
summary.pedigree

Summary of pedigree information
write.beagle

Prepare genotypic data for Beagle
discard.markers

Subsets for objects of class gpData
manhattanPlot

Manhattan plot for SNP effects
gpData2cross

Conversion between objects of class 'cross' and 'gpData'
simul.pedigree

Simulation of pedigree structure
crossVal

Cross validation of different prediction models
add.markers

Add new markers to an object of class gpData
LDDist

LD versus distance Plot
write.relationshipMatrix

Writing relationshipMatrix in table format
create.pedigree

Create pedigree object
plotNeighbourLD

Plot neighbour linkage disequilibrium
summary.gpMod

Summary for class gpMod
predict.gpMod

Prediction for genomic prediction models.
simul.phenotype

Simulation of a field trial with single trait
codeGeno

Recode genotypic data, imputation of missing values and preselection of markers
gpData2data.frame

Merge of phenotypic and genotypic data
gpMod

Genomic predictions models for objects of class gpData
plot.pedigree

Visualization of pedigree
write.plink

Prepare data for PLINK
summary.relationshipMatrix

Summary of relationship matrices
create.gpData

Create genomic prediction data object
add.individuals

Add new individuals to objects of class gpData
MME

Mixed Model Equations
pairwiseLD

Pairwise LD between markers
summary.cvData

Summary of options and results of the cross validation procedure
summaryGenMap

Summary of marker map information
kin

Relatedness based on pedigree or marker data
plotGenMap

Plot marker map
summary.gpData

Summary for class gpData
plot.relationshipMatrix

Heatmap for relationship Matrix