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synbreed (version 0.11-8)

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 (www.synbreed.tum.de). 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

20

Version

0.11-8

License

GPL-3

Maintainer

Valentin Wimmer

Last Published

June 8th, 2015

Functions in synbreed (0.11-8)

plot.pedigree

Visualization of pedigree
summary.relationshipMatrix

Summary of relationship matrices
plot.relationshipMatrix

Heatmap for relationship Matrix
gpData2data.frame

Merge of phenotypic and genotypic data
summary.gpMod

Summary for class gpMod
[.relationshipMatrix

Extract or replace part of relationship matrix
LDMap

LD Heatmap
plot.LDdf

Plot function for class LDdf
summary.cvData

Summary of options and results of the cross validation procedure
kin

Relatedness based on pedigree or marker data
add.individuals

Add new individuals to objects of class gpData
create.pedigree

Create pedigree object
simul.pedigree

Simulation of pedigree structure
codeGeno

Recode genotypic data, imputation of missing values and preselection of markers
LDDist

LD versus distance Plot
discard.markers

Subsets for objects of class gpData
summary.pedigree

Summary of pedigree information
write.plink

Prepare data for PLINK
simul.phenotype

Simulation of a field trial with single trait
create.gpData

Create genomic prediction data object
write.beagle

Prepare genotypic data for Beagle
read.vcf2matrix

Read data of a vcf-file to a matrix
manhattanPlot

Manhattan plot for SNP effects
gpMod

Genomic predictions models for objects of class gpData
plot.LDmat

Plot function for class LDmat
summaryGenMap

Summary of marker map information
write.vcf

Prepare genotypic data in vcf-Format
[.GenMap

Extract or replace part of map data.frame
MME

Mixed Model Equations
summary.LDdf

Summary for LD objects
pairwiseLD

Pairwise LD between markers
crossVal

Cross validation of different prediction models
gpData2cross

Conversion between objects of class 'cross' and 'gpData'
add.markers

Add new markers to an object of class gpData
read.vcf2list

Read data of a vcf-file to a matrix
summary.gpData

Summary for class gpData
predict.gpMod

Prediction for genomic prediction models.
plotGenMap

Plot marker map
plotNeighbourLD

Plot neighbour linkage disequilibrium
write.relationshipMatrix

Writing relationshipMatrix in table format