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synbreed (version 0.10-2)

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

0.10-2

License

GPL-2

Maintainer

Valentin Wimmer

Last Published

September 10th, 2014

Functions in synbreed (0.10-2)

create.gpData

Create genomic prediction data object
add.markers

Add new markers to an object of class gpData
add.individuals

Add new individuals to objects of class gpData
LDMap

LD Heatmap
discard.markers

Subsets for objects of class gpData
summary.pedigree

Summary of pedigree information
create.pedigree

Create pedigree object
kin

Relatedness based on pedigree or marker data
summaryGenMap

Summary of marker map information
[.relationshipMatrix

Extract or replace part of relationship matrix
MME

Mixed Model Equations
summary.LDdf

Summary for LD objects
plot.pedigree

Visualization of pedigree
plotNeighbourLD

Plot neighbour linkage disequilibrium
[.GenMap

Extract or replace part of map data.frame
write.beagle

Prepare genotypic data for Beagle
predict.gpMod

Prediction for genomic prediction models.
write.relationshipMatrix

Writing relationshipMatrix in table format
manhattanPlot

Manhattan plot for SNP effects
gpData2cross

Conversion between objects of class 'cross' and 'gpData'
pairwiseLD

Pairwise LD between markers
gpMod

Genomic predictions models for objects of class gpData
plot.LDmat

Plot function for class LDmat
crossVal

Cross validation of different prediction models
plot.LDdf

Plot function for class LDdf
LDDist

LD versus distance Plot
summary.gpMod

Summary for class gpMod
codeGeno

Recode genotypic data, imputation of missing values and preselection of markers
summary.gpData

Summary for class gpData
simul.phenotype

Simulation of a field trial with single trait
plotGenMap

Plot marker map
simul.pedigree

Simulation of pedigree structure
gpData2data.frame

Merge of phenotypic and genotypic data
plot.relationshipMatrix

Heatmap for relationship Matrix
summary.relationshipMatrix

Summary of relationship matrices
write.plink

Prepare data for PLINK
summary.cvData

Summary of options and results of the cross validation procedure