synbreed: Framework for the Analysis of Genomic Prediction Data using R
Version 0.12-6

A collection of functions required for genomic prediction which were developed within the Synbreed project for synergistic 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 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).

AuthorHans-Juergen Auinger, Valentin Wimmer, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Date of publication2017-04-21 13:58:04 UTC
MaintainerHans-Juergen Auinger <auinger@tum.de>
LicenseGPL-3
Version0.12-6
URL http://synbreed.r-forge.r-project.org/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("synbreed")

Popular man pages

Extract.relationshipMatrix: Extract or replace part of relationship matrix
plot.pedigree: Visualization of pedigree
summary.LDdf: Summary for LD objects
summary.map: Summary of marker map information
summary.pedigree: Summary of pedigree information
summary.relationshipMatrix: Summary of relationship matrices
write.beagle: Prepare genotypic data for Beagle
See all...

All man pages Function index File listing

Man pages

add.individuals: Add new individuals to objects of class gpData
add.markers: Add new markers to an object of class gpData
add.pedigree: Merge 'pedigree' object
codeGeno: Recode genotypic data, imputation of missing values and...
create.gpData: Create genomic prediction data object
create.pedigree: Create pedigree object
crossVal: Cross validation of different prediction models
discard.individuals: Subsets for objects of class gpData
discard.markers: Subsets for objects of class gpData
Extract.GenMap: Extract or replace part of map data.frame
Extract.relationshipMatrix: Extract or replace part of relationship matrix
gpData2cross: Conversion between objects of class 'cross' and 'gpData'
gpData2data.frame: Merge of phenotypic and genotypic data
gpMod: Genomic predictions models for objects of class gpData
kinship: Relatedness based on pedigree or marker data
LD: Pairwise LD between markers
LDDist: LD versus distance Plot
LDMap: LD Heatmap
manhattanPlot: Manhattan plot for SNP effects
MME: Mixed Model Equations
plot.genMap: Plot marker map
plot.LDdf: Plot function for class 'LDdf'
plot.LDmat: Plot function for class 'LDmat'
plotNeighbourLD: Plot neighbour linkage disequilibrium
plot.pedigree: Visualization of pedigree
plot.relationshipMatrix: Heatmap for relationship Matrix
predict.gpMod: Prediction for genomic prediction models.
read.vcf2list: Read data of a vcf-file to a matrix
read.vcf2matrix: Read data of a vcf-file to a matrix
simul.pedigree: Simulation of pedigree structure
simul.phenotype: Simulation of a field trial with single trait
summary.cvData: Summary of options and results of the cross validation...
summary.gpData: Summary for class gpData
summary.gpMod: Summary for class gpMod
summary.LDdf: Summary for LD objects
summary.map: Summary of marker map information
summary.pedigree: Summary of pedigree information
summary.relationshipMatrix: Summary of relationship matrices
write.beagle: Prepare genotypic data for Beagle
write.plink: Prepare data for PLINK
write.relationshipMatrix: Writing relationshipMatrix in table format
write.vcf: Prepare genotypic data in vcf-Format

Functions

LDDist Man page Source code
LDMap Man page Source code
MME Man page Source code
[.GenMap Man page
[.relationshipMatrix Man page
add.individuals Man page Source code
add.markers Man page Source code
add.pedigree Man page Source code
codeGeno Man page Source code
create.gpData Man page Source code
create.pedigree Man page Source code
cross2gpData Man page Source code
crossVal Man page Source code
discard.individuals Man page Source code
discard.markers Man page Source code
gpData2cross Man page Source code
gpData2data.frame Man page Source code
gpMod Man page Source code
kin Man page Source code
manhattanPlot Man page Source code
pairwiseLD Man page Source code
plot.GenMap Man page Source code
plot.LDdf Man page Source code
plot.LDmat Man page Source code
plot.pedigree Man page Source code
plot.relationshipMatrix Man page Source code
plotGenMap Man page Source code
plotNeighbourLD Man page Source code
predict.gpMod Man page Source code
print.summary.cvData Man page Source code
print.summary.gpData Man page Source code
print.summary.gpMod Man page Source code
print.summary.gpModList Man page Source code
print.summary.pedigree Man page Source code
print.summary.relationshipMatrix Man page Source code
read.vcf2list Man page Source code
read.vcf2matrix Man page Source code
simul.pedigree Man page Source code
simul.phenotype Man page Source code
summary.LDdf Man page Source code
summary.LDmat Man page Source code
summary.cvData Man page Source code
summary.gpData Man page Source code
summary.gpMod Man page Source code
summary.gpModList Man page Source code
summary.pedigree Man page Source code
summary.relationshipMatrix Man page Source code
summaryGenMap Man page Source code
write.beagle Man page Source code
write.plink Man page Source code
write.relationshipMatrix Man page Source code
write.vcf Man page Source code

Files

inst
inst/CITATION
inst/java
inst/java/beagle.21Jan17.6cc.jar
inst/doc
inst/doc/IntroSyn.R
inst/doc/IntroSyn.pdf
inst/doc/IntroSyn.Rnw
NAMESPACE
demo
demo/gpTest.R
demo/gpMaize.R
demo/00Index
demo/kinship.R
demo/createWheat.R
NEWS
R
R/simul.phenotype.r
R/summary.LD.r
R/cross2gpData.r
R/LD.r
R/summary.gpData.r
R/gpData2cross.r
R/manhattanPlot.r
R/gpMod.r
R/gpData2data.frame.r
R/kinship.r
R/summary.relationshipMatrix.r
R/read.write.vcf.r
R/plot.neighbourLD.r
R/plot.LDdf.LDmat.r
R/LDDist.r
R/Extract.classes.r
R/summary.pedigree.r
R/write.relationshipMatrix.r
R/plot.relationshipMatrix.r
R/LDMap.r
R/write.plink.r
R/summary.map.r
R/simul.pedigree.r
R/add.individuals.r
R/create.pedigree.r
R/add.markers.r
R/plot.pedigree.r
R/create.gpData.r
R/add.pedigree.r
R/plot.genMap.r
R/codeGeno.r
R/write.beagle.r
R/crossVal.r
R/discard.markers.r
R/predict.gpMod.r
R/MME.r
R/summary.cvData.r
vignettes
vignettes/Makefile
vignettes/bm.sty
vignettes/IntroSyn.Rnw
vignettes/figs
vignettes/figs/genMapMaize.pdf
vignettes/figs/maizeHist.pdf
vignettes/figs/relMatA.png
vignettes/figs/synbreedPackageDescription.pdf
vignettes/figs/LDmaize.png
vignettes/figs/miceHist.pdf
vignettes/figs/relMatG.png
vignettes/figs/genMapCattle.pdf
vignettes/figs/genMapMice.pdf
vignettes/figs/cattleHist.pdf
vignettes/figs/manhattanPlot.pdf
vignettes/IntroSyn.bib
vignettes/IntroSyn.tex
vignettes/cv.mice.Rdata
MD5
java
java/beagle.21Jan17.6cc.src
java/beagle.21Jan17.6cc.src/src
java/beagle.21Jan17.6cc.src/src/sample
java/beagle.21Jan17.6cc.src/src/sample/SamplerData.java
java/beagle.21Jan17.6cc.src/src/sample/HapBaumLevel.java
java/beagle.21Jan17.6cc.src/src/sample/LSHapBaum.java
java/beagle.21Jan17.6cc.src/src/sample/SingleBaumInterface.java
java/beagle.21Jan17.6cc.src/src/sample/HapNodes.java
java/beagle.21Jan17.6cc.src/src/sample/RecombSingleBaum.java
java/beagle.21Jan17.6cc.src/src/sample/RefHapSeg.java
java/beagle.21Jan17.6cc.src/src/sample/SingleBaum.java
java/beagle.21Jan17.6cc.src/src/sample/RecombSingleBaumLevel.java
java/beagle.21Jan17.6cc.src/src/sample/SingleBaumLevel.java
java/beagle.21Jan17.6cc.src/src/sample/RecombSingleNodes.java
java/beagle.21Jan17.6cc.src/src/sample/RestrictedDag.java
java/beagle.21Jan17.6cc.src/src/sample/SingleNodes.java
java/beagle.21Jan17.6cc.src/src/sample/DuoNodes.java
java/beagle.21Jan17.6cc.src/src/sample/ConsumeSingleSamples.java
java/beagle.21Jan17.6cc.src/src/sample/DiploidStates.java
java/beagle.21Jan17.6cc.src/src/sample/RefHapSegs.java
java/beagle.21Jan17.6cc.src/src/sample/DuoBaumLevel.java
java/beagle.21Jan17.6cc.src/src/sample/ImputationData.java
java/beagle.21Jan17.6cc.src/src/sample/HaplotypeCoder.java
java/beagle.21Jan17.6cc.src/src/dag
java/beagle.21Jan17.6cc.src/src/dag/Score.java
java/beagle.21Jan17.6cc.src/src/dag/DagLevel.java
java/beagle.21Jan17.6cc.src/src/dag/Dag.java
java/beagle.21Jan17.6cc.src/src/dag/LowCapacityDagLevel.java
java/beagle.21Jan17.6cc.src/src/dag/LinkageEquilibriumDag.java
java/beagle.21Jan17.6cc.src/src/dag/HighCapacityDagLevel.java
java/beagle.21Jan17.6cc.src/src/dag/MergeableDag.java
java/beagle.21Jan17.6cc.src/src/dag/ImmutableDag.java
java/beagle.21Jan17.6cc.src/src/dag/MergeableDagLevel.java
java/beagle.21Jan17.6cc.src/src/dag/DagUtil.java
java/beagle.21Jan17.6cc.src/src/vcf
java/beagle.21Jan17.6cc.src/src/vcf/VcfRecGTParser.java
java/beagle.21Jan17.6cc.src/src/vcf/GprobsStatistics.java
java/beagle.21Jan17.6cc.src/src/vcf/Bref.java
java/beagle.21Jan17.6cc.src/src/vcf/Data.java
java/beagle.21Jan17.6cc.src/src/vcf/LowMafRefGT.java
java/beagle.21Jan17.6cc.src/src/vcf/MaskedEndsGL.java
java/beagle.21Jan17.6cc.src/src/vcf/SplicedGL.java
java/beagle.21Jan17.6cc.src/src/vcf/Marker.java
java/beagle.21Jan17.6cc.src/src/vcf/SeqCodedRefGT.java
java/beagle.21Jan17.6cc.src/src/vcf/BitSetGT.java
java/beagle.21Jan17.6cc.src/src/vcf/HbdAL.java
java/beagle.21Jan17.6cc.src/src/vcf/Markers.java
java/beagle.21Jan17.6cc.src/src/vcf/AL.java
java/beagle.21Jan17.6cc.src/src/vcf/VcfIt.java
java/beagle.21Jan17.6cc.src/src/vcf/R2Estimator.java
java/beagle.21Jan17.6cc.src/src/vcf/NoPhaseGL.java
java/beagle.21Jan17.6cc.src/src/vcf/TargetData.java
java/beagle.21Jan17.6cc.src/src/vcf/VcfEmissionCompressor.java
java/beagle.21Jan17.6cc.src/src/vcf/LowMafRefDiallelicGT.java
java/beagle.21Jan17.6cc.src/src/vcf/RevGL.java
java/beagle.21Jan17.6cc.src/src/vcf/MarkerContainer.java
java/beagle.21Jan17.6cc.src/src/vcf/BasicMarker.java
java/beagle.21Jan17.6cc.src/src/vcf/VcfRecBuilder.java
java/beagle.21Jan17.6cc.src/src/vcf/IntervalVcfIt.java
java/beagle.21Jan17.6cc.src/src/vcf/FuzzyGL.java
java/beagle.21Jan17.6cc.src/src/vcf/VcfMetaInfo.java
java/beagle.21Jan17.6cc.src/src/vcf/AllData.java
java/beagle.21Jan17.6cc.src/src/vcf/RefGL.java
java/beagle.21Jan17.6cc.src/src/vcf/BitSetRefGT.java
java/beagle.21Jan17.6cc.src/src/vcf/HapsMarker.java
java/beagle.21Jan17.6cc.src/src/vcf/ByteArrayRefGT.java
java/beagle.21Jan17.6cc.src/src/vcf/VcfHeader.java
java/beagle.21Jan17.6cc.src/src/vcf/FilterUtil.java
java/beagle.21Jan17.6cc.src/src/vcf/RefIt.java
java/beagle.21Jan17.6cc.src/src/vcf/BasicGL.java
java/beagle.21Jan17.6cc.src/src/vcf/VcfEmission.java
java/beagle.21Jan17.6cc.src/src/vcf/RestrictedVcfWindow.java
java/beagle.21Jan17.6cc.src/src/vcf/VcfWindow.java
java/beagle.21Jan17.6cc.src/src/vcf/VcfRecord.java
java/beagle.21Jan17.6cc.src/src/vcf/BrefIt.java
java/beagle.21Jan17.6cc.src/src/vcf/VcfWriter.java
java/beagle.21Jan17.6cc.src/src/vcf/GL.java
java/beagle.21Jan17.6cc.src/src/haplotype
java/beagle.21Jan17.6cc.src/src/haplotype/HapPairs.java
java/beagle.21Jan17.6cc.src/src/haplotype/WrappedHapPair.java
java/beagle.21Jan17.6cc.src/src/haplotype/RevSampleHapPairs.java
java/beagle.21Jan17.6cc.src/src/haplotype/Weights.java
java/beagle.21Jan17.6cc.src/src/haplotype/GLSampleHapPairs.java
java/beagle.21Jan17.6cc.src/src/haplotype/RevHapPairs.java
java/beagle.21Jan17.6cc.src/src/haplotype/BitHapPair.java
java/beagle.21Jan17.6cc.src/src/haplotype/ConsensusPhaser.java
java/beagle.21Jan17.6cc.src/src/haplotype/RefHapPairs.java
java/beagle.21Jan17.6cc.src/src/haplotype/HapPair.java
java/beagle.21Jan17.6cc.src/src/haplotype/RevHapPair.java
java/beagle.21Jan17.6cc.src/src/haplotype/GenotypeCorrection.java
java/beagle.21Jan17.6cc.src/src/haplotype/SampleHapPairs.java
java/beagle.21Jan17.6cc.src/src/haplotype/HapsMarkerIterator.java
java/beagle.21Jan17.6cc.src/src/haplotype/BasicHapPairs.java
java/beagle.21Jan17.6cc.src/src/haplotype/BasicSampleHapPairs.java
java/beagle.21Jan17.6cc.src/src/main
java/beagle.21Jan17.6cc.src/src/main/CurrentData.java
java/beagle.21Jan17.6cc.src/src/main/HapPairSampler.java
java/beagle.21Jan17.6cc.src/src/main/RecombHapPairSampler.java
java/beagle.21Jan17.6cc.src/src/main/GeneticMap.java
java/beagle.21Jan17.6cc.src/src/main/PlinkGeneticMap.java
java/beagle.21Jan17.6cc.src/src/main/WindowWriter.java
java/beagle.21Jan17.6cc.src/src/main/NuclearFamilies.java
java/beagle.21Jan17.6cc.src/src/main/ConstrainedAlleleProbs.java
java/beagle.21Jan17.6cc.src/src/main/Par.java
java/beagle.21Jan17.6cc.src/src/main/RevGenotypeValues.java
java/beagle.21Jan17.6cc.src/src/main/LiAndStephensHapSampler.java
java/beagle.21Jan17.6cc.src/src/main/RunStats.java
java/beagle.21Jan17.6cc.src/src/main/MainHelper.java
java/beagle.21Jan17.6cc.src/src/main/GenotypeValues.java
java/beagle.21Jan17.6cc.src/src/main/LowMemHapAlleleProbs.java
java/beagle.21Jan17.6cc.src/src/main/SampleGenotypeValues.java
java/beagle.21Jan17.6cc.src/src/main/HapAlleleProbs.java
java/beagle.21Jan17.6cc.src/src/main/BasicGenotypeValues.java
java/beagle.21Jan17.6cc.src/src/main/PositionMap.java
java/beagle.21Jan17.6cc.src/src/main/SampleHapPairAlleleProbs.java
java/beagle.21Jan17.6cc.src/src/main/AlleleProbs.java
java/beagle.21Jan17.6cc.src/src/main/Main.java
java/beagle.21Jan17.6cc.src/src/main/BasicAlleleProbs.java
java/beagle.21Jan17.6cc.src/src/gpl_license
java/beagle.21Jan17.6cc.src/src/blbutil
java/beagle.21Jan17.6cc.src/src/blbutil/ByteIndexArray.java
java/beagle.21Jan17.6cc.src/src/blbutil/StringUtil.java
java/beagle.21Jan17.6cc.src/src/blbutil/BGZIPOutputStream.java
java/beagle.21Jan17.6cc.src/src/blbutil/Validate.java
java/beagle.21Jan17.6cc.src/src/blbutil/SampleFileIt.java
java/beagle.21Jan17.6cc.src/src/blbutil/IndexSet.java
java/beagle.21Jan17.6cc.src/src/blbutil/Filter.java
java/beagle.21Jan17.6cc.src/src/blbutil/IntList.java
java/beagle.21Jan17.6cc.src/src/blbutil/InputIt.java
java/beagle.21Jan17.6cc.src/src/blbutil/CharIndexArray.java
java/beagle.21Jan17.6cc.src/src/blbutil/IntArray.java
java/beagle.21Jan17.6cc.src/src/blbutil/FileIt.java
java/beagle.21Jan17.6cc.src/src/blbutil/Utilities.java
java/beagle.21Jan17.6cc.src/src/blbutil/IndexMap.java
java/beagle.21Jan17.6cc.src/src/blbutil/WrappedIntArray.java
java/beagle.21Jan17.6cc.src/src/blbutil/IntPair.java
java/beagle.21Jan17.6cc.src/src/blbutil/ShiftedByteIndexArray.java
java/beagle.21Jan17.6cc.src/src/blbutil/Const.java
java/beagle.21Jan17.6cc.src/src/blbutil/IntSet.java
java/beagle.21Jan17.6cc.src/src/blbutil/FileUtil.java
java/beagle.21Jan17.6cc.src/src/ibd
java/beagle.21Jan17.6cc.src/src/ibd/HaploidIbd.java
java/beagle.21Jan17.6cc.src/src/ibd/HapSegment.java
java/beagle.21Jan17.6cc.src/src/ibd/Haplotype.java
java/beagle.21Jan17.6cc.src/src/ibd/IbdBaum.java
java/beagle.21Jan17.6cc.src/src/ibd/IbdSegment.java
java/beagle.21Jan17.6cc.src/src/ibd/IbsHapSegments.java
java/beagle.21Jan17.6cc.src/src/beagleutil
java/beagle.21Jan17.6cc.src/src/beagleutil/BasicIntInterval.java
java/beagle.21Jan17.6cc.src/src/beagleutil/Phase.java
java/beagle.21Jan17.6cc.src/src/beagleutil/SampleIds.java
java/beagle.21Jan17.6cc.src/src/beagleutil/ChromIds.java
java/beagle.21Jan17.6cc.src/src/beagleutil/ThreadSafeIndexer.java
java/beagle.21Jan17.6cc.src/src/beagleutil/IntIntervalTree.java
java/beagle.21Jan17.6cc.src/src/beagleutil/IntInterval.java
java/beagle.21Jan17.6cc.src/src/beagleutil/ChromInterval.java
java/beagle.21Jan17.6cc.src/src/beagleutil/CenteredIntIntervalTree.java
java/beagle.21Jan17.6cc.src/src/beagleutil/Samples.java
java/beagle.21Jan17.6cc.src/src/net
java/beagle.21Jan17.6cc.src/src/net/sf
java/beagle.21Jan17.6cc.src/src/net/sf/samtools
java/beagle.21Jan17.6cc.src/src/net/sf/samtools/SAMFormatException.java
java/beagle.21Jan17.6cc.src/src/net/sf/samtools/FileTruncatedException.java
java/beagle.21Jan17.6cc.src/src/net/sf/samtools/SAMException.java
java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util
java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/RuntimeEOFException.java
java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/BlockCompressedFilePointerUtil.java
java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/BlockCompressedInputStream.java
java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/StringUtil.java
java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/SeekableStream.java
java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/RuntimeIOException.java
java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/BlockCompressedStreamConstants.java
java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/SeekableHTTPStream.java
java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/SeekableFileStream.java
java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/BlockCompressedOutputStream.java
java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/BinaryCodec.java
java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/IOUtil.java
java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/BlockGunzipper.java
java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/HttpUtils.java
java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/SeekableBufferedStream.java
java/beagle.21Jan17.6cc.src/src/net/sf/samtools/Defaults.java
java/COPYRIGHTS
build
build/vignette.rds
DESCRIPTION
man
man/MME.Rd
man/add.pedigree.Rd
man/summary.gpMod.Rd
man/plot.genMap.Rd
man/Extract.relationshipMatrix.Rd
man/LD.Rd
man/LDMap.Rd
man/plot.relationshipMatrix.Rd
man/summary.relationshipMatrix.Rd
man/gpData2cross.Rd
man/manhattanPlot.Rd
man/create.pedigree.Rd
man/discard.markers.Rd
man/read.vcf2list.Rd
man/write.vcf.Rd
man/write.plink.Rd
man/write.relationshipMatrix.Rd
man/summary.map.Rd
man/gpMod.Rd
man/add.individuals.Rd
man/gpData2data.frame.Rd
man/codeGeno.Rd
man/summary.pedigree.Rd
man/plotNeighbourLD.Rd
man/write.beagle.Rd
man/read.vcf2matrix.Rd
man/plot.LDdf.Rd
man/predict.gpMod.Rd
man/crossVal.Rd
man/LDDist.Rd
man/kinship.Rd
man/summary.gpData.Rd
man/plot.pedigree.Rd
man/plot.LDmat.Rd
man/create.gpData.Rd
man/summary.LDdf.Rd
man/simul.pedigree.Rd
man/discard.individuals.Rd
man/summary.cvData.Rd
man/Extract.GenMap.Rd
man/simul.phenotype.Rd
man/add.markers.Rd
.Rinstignore
synbreed documentation built on May 20, 2017, 4:49 a.m.

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