Files in synbreed
Framework for the Analysis of Genomic Prediction Data using R

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 30, 2017, 7:13 a.m.