synbreed: 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).

AuthorValentin Wimmer, Hans-Juergen Auinger, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Date of publication2016-10-13 00:24:51
MaintainerHans-Juergen Auinger <auinger@tum.de>
LicenseGPL-3
Version0.11-41
http://synbreed.r-forge.r-project.org/

View on CRAN

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

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

Files

synbreed
synbreed/inst
synbreed/inst/CITATION
synbreed/inst/java
synbreed/inst/java/beagle.r1399.jar
synbreed/inst/doc
synbreed/inst/doc/IntroSyn.R
synbreed/inst/doc/IntroSyn.pdf
synbreed/inst/doc/IntroSyn.Rnw
synbreed/NAMESPACE
synbreed/demo
synbreed/demo/gpTest.R
synbreed/demo/gpMaize.R
synbreed/demo/00Index
synbreed/demo/kinship.R
synbreed/demo/createWheat.R
synbreed/NEWS
synbreed/R
synbreed/R/simul.phenotype.r
synbreed/R/summary.LD.r
synbreed/R/cross2gpData.r
synbreed/R/LD.r
synbreed/R/summary.gpData.r
synbreed/R/gpData2cross.r
synbreed/R/manhattanPlot.r
synbreed/R/gpMod.r
synbreed/R/gpData2data.frame.r
synbreed/R/kinship.r
synbreed/R/summary.relationshipMatrix.r
synbreed/R/read.write.vcf.r
synbreed/R/plot.neighbourLD.r
synbreed/R/plot.LDdf.LDmat.r
synbreed/R/LDDist.r
synbreed/R/Extract.classes.r
synbreed/R/summary.pedigree.r
synbreed/R/write.relationshipMatrix.r
synbreed/R/plot.relationshipMatrix.r
synbreed/R/LDMap.r
synbreed/R/write.plink.r
synbreed/R/summary.map.r
synbreed/R/simul.pedigree.r
synbreed/R/create.pedigree.r
synbreed/R/add.markers.r
synbreed/R/plot.pedigree.r
synbreed/R/create.gpData.r
synbreed/R/add.pedigree.r
synbreed/R/plot.genMap.r
synbreed/R/codeGeno.r
synbreed/R/write.beagle.r
synbreed/R/crossVal.r
synbreed/R/discard.markers.r
synbreed/R/predict.gpMod.r
synbreed/R/MME.r
synbreed/R/summary.cvData.r
synbreed/vignettes
synbreed/vignettes/Makefile
synbreed/vignettes/bm.sty
synbreed/vignettes/IntroSyn.Rnw
synbreed/vignettes/figs
synbreed/vignettes/figs/genMapMaize.pdf
synbreed/vignettes/figs/maizeHist.pdf
synbreed/vignettes/figs/relMatA.png
synbreed/vignettes/figs/synbreedPackageDescription.pdf
synbreed/vignettes/figs/LDmaize.png
synbreed/vignettes/figs/miceHist.pdf
synbreed/vignettes/figs/relMatG.png
synbreed/vignettes/figs/genMapCattle.pdf
synbreed/vignettes/figs/genMapMice.pdf
synbreed/vignettes/figs/cattleHist.pdf
synbreed/vignettes/figs/manhattanPlot.pdf
synbreed/vignettes/IntroSyn.bib
synbreed/vignettes/IntroSyn.tex
synbreed/vignettes/cv.mice.Rdata
synbreed/MD5
synbreed/java
synbreed/java/beagle.r1399.src
synbreed/java/beagle.r1399.src/src
synbreed/java/beagle.r1399.src/src/sample
synbreed/java/beagle.r1399.src/src/sample/HapBaumLevel.java
synbreed/java/beagle.r1399.src/src/sample/TrioBaumLevel.java
synbreed/java/beagle.r1399.src/src/sample/TrioNodes.java
synbreed/java/beagle.r1399.src/src/sample/SingleBaumInterface.java
synbreed/java/beagle.r1399.src/src/sample/HapNodes.java
synbreed/java/beagle.r1399.src/src/sample/ProduceHapSamples.java
synbreed/java/beagle.r1399.src/src/sample/SingleBaum.java
synbreed/java/beagle.r1399.src/src/sample/SingleBaumLevel.java
synbreed/java/beagle.r1399.src/src/sample/ProduceSingleSamples.java
synbreed/java/beagle.r1399.src/src/sample/SingleNodes.java
synbreed/java/beagle.r1399.src/src/sample/DuoNodes.java
synbreed/java/beagle.r1399.src/src/sample/HapBaum.java
synbreed/java/beagle.r1399.src/src/sample/DuoBaum.java
synbreed/java/beagle.r1399.src/src/sample/DuoBaumLevel.java
synbreed/java/beagle.r1399.src/src/sample/TrioBaum.java
synbreed/java/beagle.r1399.src/src/dag
synbreed/java/beagle.r1399.src/src/dag/Score.java
synbreed/java/beagle.r1399.src/src/dag/DagLevel.java
synbreed/java/beagle.r1399.src/src/dag/ImmutableDagLevel.java
synbreed/java/beagle.r1399.src/src/dag/Dag.java
synbreed/java/beagle.r1399.src/src/dag/LinkageEquilibriumDag.java
synbreed/java/beagle.r1399.src/src/dag/MergeableDag.java
synbreed/java/beagle.r1399.src/src/dag/ImmutableDag.java
synbreed/java/beagle.r1399.src/src/dag/MergeableDagLevel.java
synbreed/java/beagle.r1399.src/src/dag/DagUtils.java
synbreed/java/beagle.r1399.src/src/vcf
synbreed/java/beagle.r1399.src/src/vcf/Data.java
synbreed/java/beagle.r1399.src/src/vcf/VcfIterator.java
synbreed/java/beagle.r1399.src/src/vcf/MarkerFilterUtils.java
synbreed/java/beagle.r1399.src/src/vcf/ImputationGL.java
synbreed/java/beagle.r1399.src/src/vcf/Marker.java
synbreed/java/beagle.r1399.src/src/vcf/BitSetGT.java
synbreed/java/beagle.r1399.src/src/vcf/HbdAL.java
synbreed/java/beagle.r1399.src/src/vcf/Markers.java
synbreed/java/beagle.r1399.src/src/vcf/IntervalVcfIterator.java
synbreed/java/beagle.r1399.src/src/vcf/AL.java
synbreed/java/beagle.r1399.src/src/vcf/NoPhaseGL.java
synbreed/java/beagle.r1399.src/src/vcf/RevGL.java
synbreed/java/beagle.r1399.src/src/vcf/RevAL.java
synbreed/java/beagle.r1399.src/src/vcf/VcfEmissionFactory.java
synbreed/java/beagle.r1399.src/src/vcf/VcfEmissionIterator.java
synbreed/java/beagle.r1399.src/src/vcf/VcfMetaInfo.java
synbreed/java/beagle.r1399.src/src/vcf/AllData.java
synbreed/java/beagle.r1399.src/src/vcf/RefGL.java
synbreed/java/beagle.r1399.src/src/vcf/BitSetRefGT.java
synbreed/java/beagle.r1399.src/src/vcf/VcfHeader.java
synbreed/java/beagle.r1399.src/src/vcf/NonRefData.java
synbreed/java/beagle.r1399.src/src/vcf/BasicGL.java
synbreed/java/beagle.r1399.src/src/vcf/VcfEmission.java
synbreed/java/beagle.r1399.src/src/vcf/HapAL.java
synbreed/java/beagle.r1399.src/src/vcf/MedMemGL.java
synbreed/java/beagle.r1399.src/src/vcf/MedMemGTGL.java
synbreed/java/beagle.r1399.src/src/vcf/VcfRefIterator.java
synbreed/java/beagle.r1399.src/src/vcf/VcfWindow.java
synbreed/java/beagle.r1399.src/src/vcf/VcfRecord.java
synbreed/java/beagle.r1399.src/src/vcf/VcfWriter.java
synbreed/java/beagle.r1399.src/src/vcf/GL.java
synbreed/java/beagle.r1399.src/src/vcf/FilteredVcfIterator.java
synbreed/java/beagle.r1399.src/src/haplotype
synbreed/java/beagle.r1399.src/src/haplotype/HapPairs.java
synbreed/java/beagle.r1399.src/src/haplotype/WrappedHapPair.java
synbreed/java/beagle.r1399.src/src/haplotype/Weights.java
synbreed/java/beagle.r1399.src/src/haplotype/SampleHapPairsSplicer.java
synbreed/java/beagle.r1399.src/src/haplotype/BitHapPair.java
synbreed/java/beagle.r1399.src/src/haplotype/RefHapPairs.java
synbreed/java/beagle.r1399.src/src/haplotype/HapPair.java
synbreed/java/beagle.r1399.src/src/haplotype/RevHapPair.java
synbreed/java/beagle.r1399.src/src/haplotype/HapsMarker.java
synbreed/java/beagle.r1399.src/src/haplotype/ConsensusPhasing.java
synbreed/java/beagle.r1399.src/src/haplotype/SampleHapPairs.java
synbreed/java/beagle.r1399.src/src/haplotype/HapsMarkerIterator.java
synbreed/java/beagle.r1399.src/src/haplotype/BasicHapPairs.java
synbreed/java/beagle.r1399.src/src/haplotype/BasicSampleHapPairs.java
synbreed/java/beagle.r1399.src/src/main
synbreed/java/beagle.r1399.src/src/main/HapPairSampler.java
synbreed/java/beagle.r1399.src/src/main/GprobsStatistics.java
synbreed/java/beagle.r1399.src/src/main/Logger.java
synbreed/java/beagle.r1399.src/src/main/GeneticMap.java
synbreed/java/beagle.r1399.src/src/main/WindowWriter.java
synbreed/java/beagle.r1399.src/src/main/NuclearFamilies.java
synbreed/java/beagle.r1399.src/src/main/RevGenotypeValues.java
synbreed/java/beagle.r1399.src/src/main/RunStats.java
synbreed/java/beagle.r1399.src/src/main/MainHelper.java
synbreed/java/beagle.r1399.src/src/main/GenotypeValues.java
synbreed/java/beagle.r1399.src/src/main/RestrictedGenotypeValues.java
synbreed/java/beagle.r1399.src/src/main/SampleGenotypeValues.java
synbreed/java/beagle.r1399.src/src/main/BasicGenotypeValues.java
synbreed/java/beagle.r1399.src/src/main/FixedGenotypeValues.java
synbreed/java/beagle.r1399.src/src/main/Parameters.java
synbreed/java/beagle.r1399.src/src/main/Main.java
synbreed/java/beagle.r1399.src/src/gpl_license
synbreed/java/beagle.r1399.src/src/blbutil
synbreed/java/beagle.r1399.src/src/blbutil/StringUtil.java
synbreed/java/beagle.r1399.src/src/blbutil/Pair.java
synbreed/java/beagle.r1399.src/src/blbutil/Validate.java
synbreed/java/beagle.r1399.src/src/blbutil/FilterUtils.java
synbreed/java/beagle.r1399.src/src/blbutil/IndexSet.java
synbreed/java/beagle.r1399.src/src/blbutil/SampleFileIterator.java
synbreed/java/beagle.r1399.src/src/blbutil/FileIterator.java
synbreed/java/beagle.r1399.src/src/blbutil/Filter.java
synbreed/java/beagle.r1399.src/src/blbutil/IntList.java
synbreed/java/beagle.r1399.src/src/blbutil/InputIterator.java
synbreed/java/beagle.r1399.src/src/blbutil/Utilities.java
synbreed/java/beagle.r1399.src/src/blbutil/IndexMap.java
synbreed/java/beagle.r1399.src/src/blbutil/IntPair.java
synbreed/java/beagle.r1399.src/src/blbutil/Const.java
synbreed/java/beagle.r1399.src/src/blbutil/FileUtil.java
synbreed/java/beagle.r1399.src/src/ibd
synbreed/java/beagle.r1399.src/src/ibd/HaploidIbd.java
synbreed/java/beagle.r1399.src/src/ibd/HapSegment.java
synbreed/java/beagle.r1399.src/src/ibd/Haplotype.java
synbreed/java/beagle.r1399.src/src/ibd/IbdBaum.java
synbreed/java/beagle.r1399.src/src/ibd/IbdSegment.java
synbreed/java/beagle.r1399.src/src/ibd/IbsHapSegments.java
synbreed/java/beagle.r1399.src/src/beagleutil
synbreed/java/beagle.r1399.src/src/beagleutil/Phase.java
synbreed/java/beagle.r1399.src/src/beagleutil/SampleIds.java
synbreed/java/beagle.r1399.src/src/beagleutil/ChromIds.java
synbreed/java/beagle.r1399.src/src/beagleutil/IntInterval.java
synbreed/java/beagle.r1399.src/src/beagleutil/Ids.java
synbreed/java/beagle.r1399.src/src/beagleutil/ChromInterval.java
synbreed/java/beagle.r1399.src/src/beagleutil/Samples.java
synbreed/java/beagle.r1399.src/src/net
synbreed/java/beagle.r1399.src/src/net/sf
synbreed/java/beagle.r1399.src/src/net/sf/samtools
synbreed/java/beagle.r1399.src/src/net/sf/samtools/SAMFormatException.java
synbreed/java/beagle.r1399.src/src/net/sf/samtools/FileTruncatedException.java
synbreed/java/beagle.r1399.src/src/net/sf/samtools/SAMException.java
synbreed/java/beagle.r1399.src/src/net/sf/samtools/util
synbreed/java/beagle.r1399.src/src/net/sf/samtools/util/RuntimeEOFException.java
synbreed/java/beagle.r1399.src/src/net/sf/samtools/util/BlockCompressedFilePointerUtil.java
synbreed/java/beagle.r1399.src/src/net/sf/samtools/util/BlockCompressedInputStream.java
synbreed/java/beagle.r1399.src/src/net/sf/samtools/util/StringUtil.java
synbreed/java/beagle.r1399.src/src/net/sf/samtools/util/SeekableStream.java
synbreed/java/beagle.r1399.src/src/net/sf/samtools/util/RuntimeIOException.java
synbreed/java/beagle.r1399.src/src/net/sf/samtools/util/BlockCompressedStreamConstants.java
synbreed/java/beagle.r1399.src/src/net/sf/samtools/util/SeekableHTTPStream.java
synbreed/java/beagle.r1399.src/src/net/sf/samtools/util/SeekableFileStream.java
synbreed/java/beagle.r1399.src/src/net/sf/samtools/util/BlockCompressedOutputStream.java
synbreed/java/beagle.r1399.src/src/net/sf/samtools/util/BinaryCodec.java
synbreed/java/beagle.r1399.src/src/net/sf/samtools/util/IOUtil.java
synbreed/java/beagle.r1399.src/src/net/sf/samtools/util/BlockGunzipper.java
synbreed/java/beagle.r1399.src/src/net/sf/samtools/util/HttpUtils.java
synbreed/java/beagle.r1399.src/src/net/sf/samtools/util/SeekableBufferedStream.java
synbreed/java/beagle.r1399.src/src/net/sf/samtools/Defaults.java
synbreed/java/COPYRIGHTS
synbreed/build
synbreed/build/vignette.rds
synbreed/DESCRIPTION
synbreed/man
synbreed/man/MME.Rd synbreed/man/add.pedigree.Rd synbreed/man/summary.gpMod.Rd synbreed/man/plot.genMap.Rd synbreed/man/Extract.relationshipMatrix.Rd synbreed/man/LD.Rd synbreed/man/LDMap.Rd synbreed/man/plot.relationshipMatrix.Rd synbreed/man/summary.relationshipMatrix.Rd synbreed/man/gpData2cross.Rd synbreed/man/manhattanPlot.Rd synbreed/man/create.pedigree.Rd synbreed/man/discard.markers.Rd synbreed/man/read.vcf2list.Rd synbreed/man/write.vcf.Rd synbreed/man/write.plink.Rd synbreed/man/write.relationshipMatrix.Rd synbreed/man/summary.map.Rd synbreed/man/gpMod.Rd synbreed/man/add.individuals.Rd synbreed/man/gpData2data.frame.Rd synbreed/man/codeGeno.Rd synbreed/man/summary.pedigree.Rd synbreed/man/plotNeighbourLD.Rd synbreed/man/write.beagle.Rd synbreed/man/read.vcf2matrix.Rd synbreed/man/plot.LDdf.Rd synbreed/man/predict.gpMod.Rd synbreed/man/crossVal.Rd synbreed/man/LDDist.Rd synbreed/man/kinship.Rd synbreed/man/summary.gpData.Rd synbreed/man/plot.pedigree.Rd synbreed/man/plot.LDmat.Rd synbreed/man/create.gpData.Rd synbreed/man/summary.LDdf.Rd synbreed/man/simul.pedigree.Rd synbreed/man/discard.individuals.Rd synbreed/man/summary.cvData.Rd synbreed/man/Extract.GenMap.Rd synbreed/man/simul.phenotype.Rd synbreed/man/add.markers.Rd
synbreed/.Rinstignore

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