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synbreed (version 0.11-4)

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

0.11-4

License

GPL-3

Maintainer

Valentin Wimmer

Last Published

May 27th, 2015

Functions in synbreed (0.11-4)

read.vcf2list

Read data of a vcf-file to a matrix
gpData2data.frame

Merge of phenotypic and genotypic data
gpData2cross

Conversion between objects of class 'cross' and 'gpData'
summary.LDdf

Summary for LD objects
LDMap

LD Heatmap
write.vcf

Prepare genotypic data in vcf-Format
discard.markers

Subsets for objects of class gpData
gpMod

Genomic predictions models for objects of class gpData
add.markers

Add new markers to an object of class gpData
plot.LDmat

Plot function for class LDmat
simul.pedigree

Simulation of pedigree structure
plot.pedigree

Visualization of pedigree
[.GenMap

Extract or replace part of map data.frame
pairwiseLD

Pairwise LD between markers
predict.gpMod

Prediction for genomic prediction models.
kin

Relatedness based on pedigree or marker data
summaryGenMap

Summary of marker map information
plot.relationshipMatrix

Heatmap for relationship Matrix
summary.gpData

Summary for class gpData
plot.LDdf

Plot function for class LDdf
LDDist

LD versus distance Plot
MME

Mixed Model Equations
create.pedigree

Create pedigree object
crossVal

Cross validation of different prediction models
plotGenMap

Plot marker map
create.gpData

Create genomic prediction data object
codeGeno

Recode genotypic data, imputation of missing values and preselection of markers
write.relationshipMatrix

Writing relationshipMatrix in table format
read.vcf2matrix

Read data of a vcf-file to a matrix
write.beagle

Prepare genotypic data for Beagle
summary.cvData

Summary of options and results of the cross validation procedure
[.relationshipMatrix

Extract or replace part of relationship matrix
add.individuals

Add new individuals to objects of class gpData
plotNeighbourLD

Plot neighbour linkage disequilibrium
summary.gpMod

Summary for class gpMod
summary.pedigree

Summary of pedigree information
summary.relationshipMatrix

Summary of relationship matrices
simul.phenotype

Simulation of a field trial with single trait
write.plink

Prepare data for PLINK
manhattanPlot

Manhattan plot for SNP effects