synbreed v0.12-6

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Framework for the Analysis of Genomic Prediction Data using R

A collection of functions required for genomic prediction which were developed within the Synbreed project for synergistic plant and animal breeding (<http://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).

Functions in synbreed

Name Description
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
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Details

Type Package
Date 2017-04-21
URL http://synbreed.r-forge.r-project.org/
License GPL-3
LazyLoad yes
LazyData no
ZipData no
Repository CRAN
Repository/R-Forge/Project synbreed
Repository/R-Forge/Revision 689
Repository/R-Forge/DateTimeStamp 2017-04-21 12:23:14
Date/Publication 2017-04-21 13:58:04 UTC
NeedsCompilation no
Packaged 2017-04-21 12:25:56 UTC; rforge

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