Files in synbreed

Framework for the Analysis of Genomic Prediction Data using R

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NEWS

NAMESPACE

DESCRIPTION

java/COPYRIGHTS

java/beagle.21Jan17.6cc.src/src/gpl_license

java/beagle.21Jan17.6cc.src/src/beagleutil/ThreadSafeIndexer.java

java/beagle.21Jan17.6cc.src/src/beagleutil/SampleIds.java

java/beagle.21Jan17.6cc.src/src/beagleutil/IntIntervalTree.java

java/beagle.21Jan17.6cc.src/src/beagleutil/BasicIntInterval.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/beagleutil/ChromIds.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/Phase.java

java/beagle.21Jan17.6cc.src/src/blbutil/BGZIPOutputStream.java

java/beagle.21Jan17.6cc.src/src/blbutil/FileIt.java

java/beagle.21Jan17.6cc.src/src/blbutil/InputIt.java

java/beagle.21Jan17.6cc.src/src/blbutil/IntList.java

java/beagle.21Jan17.6cc.src/src/blbutil/Const.java

java/beagle.21Jan17.6cc.src/src/blbutil/ByteIndexArray.java

java/beagle.21Jan17.6cc.src/src/blbutil/Filter.java

java/beagle.21Jan17.6cc.src/src/blbutil/IntArray.java

java/beagle.21Jan17.6cc.src/src/blbutil/CharIndexArray.java

java/beagle.21Jan17.6cc.src/src/blbutil/IntSet.java

java/beagle.21Jan17.6cc.src/src/blbutil/Validate.java

java/beagle.21Jan17.6cc.src/src/blbutil/IntPair.java

java/beagle.21Jan17.6cc.src/src/blbutil/SampleFileIt.java

java/beagle.21Jan17.6cc.src/src/blbutil/StringUtil.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/Utilities.java

java/beagle.21Jan17.6cc.src/src/blbutil/IndexSet.java

java/beagle.21Jan17.6cc.src/src/blbutil/FileUtil.java

java/beagle.21Jan17.6cc.src/src/blbutil/ShiftedByteIndexArray.java

java/beagle.21Jan17.6cc.src/src/main/AlleleProbs.java

java/beagle.21Jan17.6cc.src/src/main/BasicAlleleProbs.java

java/beagle.21Jan17.6cc.src/src/main/CurrentData.java

java/beagle.21Jan17.6cc.src/src/main/PositionMap.java

java/beagle.21Jan17.6cc.src/src/main/Main.java

java/beagle.21Jan17.6cc.src/src/main/PlinkGeneticMap.java

java/beagle.21Jan17.6cc.src/src/main/MainHelper.java

java/beagle.21Jan17.6cc.src/src/main/BasicGenotypeValues.java

java/beagle.21Jan17.6cc.src/src/main/GenotypeValues.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/SampleHapPairAlleleProbs.java

java/beagle.21Jan17.6cc.src/src/main/LiAndStephensHapSampler.java

java/beagle.21Jan17.6cc.src/src/main/WindowWriter.java

java/beagle.21Jan17.6cc.src/src/main/HapAlleleProbs.java

java/beagle.21Jan17.6cc.src/src/main/Par.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/RunStats.java

java/beagle.21Jan17.6cc.src/src/main/HapPairSampler.java

java/beagle.21Jan17.6cc.src/src/main/NuclearFamilies.java

java/beagle.21Jan17.6cc.src/src/main/RevGenotypeValues.java

java/beagle.21Jan17.6cc.src/src/main/ConstrainedAlleleProbs.java

java/beagle.21Jan17.6cc.src/src/dag/Score.java

java/beagle.21Jan17.6cc.src/src/dag/Dag.java

java/beagle.21Jan17.6cc.src/src/dag/DagUtil.java

java/beagle.21Jan17.6cc.src/src/dag/ImmutableDag.java

java/beagle.21Jan17.6cc.src/src/dag/DagLevel.java

java/beagle.21Jan17.6cc.src/src/dag/HighCapacityDagLevel.java

java/beagle.21Jan17.6cc.src/src/dag/LowCapacityDagLevel.java

java/beagle.21Jan17.6cc.src/src/dag/MergeableDag.java

java/beagle.21Jan17.6cc.src/src/dag/MergeableDagLevel.java

java/beagle.21Jan17.6cc.src/src/dag/LinkageEquilibriumDag.java

java/beagle.21Jan17.6cc.src/src/vcf/GprobsStatistics.java

java/beagle.21Jan17.6cc.src/src/vcf/Markers.java

java/beagle.21Jan17.6cc.src/src/vcf/VcfEmission.java

java/beagle.21Jan17.6cc.src/src/vcf/VcfIt.java

java/beagle.21Jan17.6cc.src/src/vcf/AL.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/BasicGL.java

java/beagle.21Jan17.6cc.src/src/vcf/LowMafRefGT.java

java/beagle.21Jan17.6cc.src/src/vcf/RefIt.java

java/beagle.21Jan17.6cc.src/src/vcf/RevGL.java

java/beagle.21Jan17.6cc.src/src/vcf/RestrictedVcfWindow.java

java/beagle.21Jan17.6cc.src/src/vcf/SplicedGL.java

java/beagle.21Jan17.6cc.src/src/vcf/VcfRecord.java

java/beagle.21Jan17.6cc.src/src/vcf/NoPhaseGL.java

java/beagle.21Jan17.6cc.src/src/vcf/Marker.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/VcfEmissionCompressor.java

java/beagle.21Jan17.6cc.src/src/vcf/BrefIt.java

java/beagle.21Jan17.6cc.src/src/vcf/IntervalVcfIt.java

java/beagle.21Jan17.6cc.src/src/vcf/RefGL.java

java/beagle.21Jan17.6cc.src/src/vcf/VcfHeader.java

java/beagle.21Jan17.6cc.src/src/vcf/GL.java

java/beagle.21Jan17.6cc.src/src/vcf/HbdAL.java

java/beagle.21Jan17.6cc.src/src/vcf/R2Estimator.java

java/beagle.21Jan17.6cc.src/src/vcf/MaskedEndsGL.java

java/beagle.21Jan17.6cc.src/src/vcf/BitSetRefGT.java

java/beagle.21Jan17.6cc.src/src/vcf/LowMafRefDiallelicGT.java

java/beagle.21Jan17.6cc.src/src/vcf/VcfRecGTParser.java

java/beagle.21Jan17.6cc.src/src/vcf/TargetData.java

java/beagle.21Jan17.6cc.src/src/vcf/Data.java

java/beagle.21Jan17.6cc.src/src/vcf/MarkerContainer.java

java/beagle.21Jan17.6cc.src/src/vcf/BitSetGT.java

java/beagle.21Jan17.6cc.src/src/vcf/FuzzyGL.java

java/beagle.21Jan17.6cc.src/src/vcf/VcfWindow.java

java/beagle.21Jan17.6cc.src/src/vcf/FilterUtil.java

java/beagle.21Jan17.6cc.src/src/vcf/SeqCodedRefGT.java

java/beagle.21Jan17.6cc.src/src/vcf/Bref.java

java/beagle.21Jan17.6cc.src/src/vcf/ByteArrayRefGT.java

java/beagle.21Jan17.6cc.src/src/vcf/HapsMarker.java

java/beagle.21Jan17.6cc.src/src/vcf/VcfWriter.java

java/beagle.21Jan17.6cc.src/src/haplotype/RefHapPairs.java

java/beagle.21Jan17.6cc.src/src/haplotype/BasicSampleHapPairs.java

java/beagle.21Jan17.6cc.src/src/haplotype/HapPairs.java

java/beagle.21Jan17.6cc.src/src/haplotype/GenotypeCorrection.java

java/beagle.21Jan17.6cc.src/src/haplotype/Weights.java

java/beagle.21Jan17.6cc.src/src/haplotype/HapsMarkerIterator.java

java/beagle.21Jan17.6cc.src/src/haplotype/GLSampleHapPairs.java

java/beagle.21Jan17.6cc.src/src/haplotype/ConsensusPhaser.java

java/beagle.21Jan17.6cc.src/src/haplotype/RevHapPair.java

java/beagle.21Jan17.6cc.src/src/haplotype/SampleHapPairs.java

java/beagle.21Jan17.6cc.src/src/haplotype/RevHapPairs.java

java/beagle.21Jan17.6cc.src/src/haplotype/RevSampleHapPairs.java

java/beagle.21Jan17.6cc.src/src/haplotype/BasicHapPairs.java

java/beagle.21Jan17.6cc.src/src/haplotype/HapPair.java

java/beagle.21Jan17.6cc.src/src/haplotype/BitHapPair.java

java/beagle.21Jan17.6cc.src/src/haplotype/WrappedHapPair.java

java/beagle.21Jan17.6cc.src/src/sample/RestrictedDag.java

java/beagle.21Jan17.6cc.src/src/sample/RefHapSeg.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/SamplerData.java

java/beagle.21Jan17.6cc.src/src/sample/DuoNodes.java

java/beagle.21Jan17.6cc.src/src/sample/DiploidStates.java

java/beagle.21Jan17.6cc.src/src/sample/HaplotypeCoder.java

java/beagle.21Jan17.6cc.src/src/sample/ConsumeSingleSamples.java

java/beagle.21Jan17.6cc.src/src/sample/HapNodes.java

java/beagle.21Jan17.6cc.src/src/sample/HapBaumLevel.java

java/beagle.21Jan17.6cc.src/src/sample/RecombSingleBaum.java

java/beagle.21Jan17.6cc.src/src/sample/SingleBaumLevel.java

java/beagle.21Jan17.6cc.src/src/sample/RecombSingleBaumLevel.java

java/beagle.21Jan17.6cc.src/src/sample/SingleBaum.java

java/beagle.21Jan17.6cc.src/src/sample/ImputationData.java

java/beagle.21Jan17.6cc.src/src/sample/RecombSingleNodes.java

java/beagle.21Jan17.6cc.src/src/sample/SingleNodes.java

java/beagle.21Jan17.6cc.src/src/sample/SingleBaumInterface.java

java/beagle.21Jan17.6cc.src/src/sample/LSHapBaum.java

java/beagle.21Jan17.6cc.src/src/ibd/IbdSegment.java

java/beagle.21Jan17.6cc.src/src/ibd/HapSegment.java

java/beagle.21Jan17.6cc.src/src/ibd/IbdBaum.java

java/beagle.21Jan17.6cc.src/src/ibd/IbsHapSegments.java

java/beagle.21Jan17.6cc.src/src/ibd/Haplotype.java

java/beagle.21Jan17.6cc.src/src/ibd/HaploidIbd.java

java/beagle.21Jan17.6cc.src/src/net/sf/samtools/Defaults.java

java/beagle.21Jan17.6cc.src/src/net/sf/samtools/SAMFormatException.java

java/beagle.21Jan17.6cc.src/src/net/sf/samtools/SAMException.java

java/beagle.21Jan17.6cc.src/src/net/sf/samtools/FileTruncatedException.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/BlockCompressedOutputStream.java

java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/RuntimeIOException.java

java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/SeekableHTTPStream.java

java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/StringUtil.java

java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/BlockCompressedStreamConstants.java

java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/SeekableFileStream.java

java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/RuntimeEOFException.java

java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/BlockCompressedInputStream.java

java/beagle.21Jan17.6cc.src/src/net/sf/samtools/util/BlockCompressedFilePointerUtil.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/util/SeekableStream.java

R/plot.genMap.r R/summary.relationshipMatrix.r R/write.relationshipMatrix.r R/gpData2data.frame.r R/add.pedigree.r R/codeGeno.r R/discard.markers.r R/summary.LD.r R/simul.pedigree.r R/plot.neighbourLD.r R/summary.cvData.r R/manhattanPlot.r R/plot.pedigree.r R/gpMod.r R/gpData2cross.r R/create.pedigree.r R/crossVal.r R/summary.gpData.r R/write.plink.r R/kinship.r R/Extract.classes.r R/MME.r R/LD.r R/LDDist.r R/simul.phenotype.r R/create.gpData.r R/LDMap.r R/write.beagle.r R/summary.map.r R/add.gpData.r R/plot.relationshipMatrix.r R/predict.gpMod.r R/summary.pedigree.r R/read.write.vcf.r R/cross2gpData.r R/add.markers.r R/add.individuals.r R/plot.LDdf.LDmat.r

inst/CITATION

inst/doc/IntroSyn.Rnw

inst/doc/IntroSyn.pdf inst/doc/IntroSyn.R

inst/java/beagle.21Jan17.6cc.jar

demo/createWheat.R demo/kinship.R demo/gpTest.R

demo/00Index

demo/gpMaize.R

build/vignette.rds

vignettes/IntroSyn.Rnw

vignettes/bm.sty

vignettes/IntroSyn.tex

vignettes/IntroSyn.bib

vignettes/Makefile

vignettes/cv.mice.Rdata

vignettes/figs/genMapMice.pdf vignettes/figs/cattleHist.pdf vignettes/figs/genMapCattle.pdf vignettes/figs/manhattanPlot.pdf

vignettes/figs/LDmaize.png

vignettes/figs/genMapMaize.pdf vignettes/figs/synbreedPackageDescription.pdf

vignettes/figs/relMatA.png

vignettes/figs/miceHist.pdf

vignettes/figs/relMatG.png

vignettes/figs/maizeHist.pdf

data/datalist

data/maize.RData

data/mice.RData

data/cattle.RData

man/Extract.relationshipMatrix.Rd man/codeGeno.Rd man/plotNeighbourLD.Rd man/write.plink.Rd man/add.pedigree.Rd man/summary.relationshipMatrix.Rd man/add.individuals.Rd man/write.beagle.Rd man/manhattanPlot.Rd man/LD.Rd man/MME.Rd man/add.markers.Rd man/summary.pedigree.Rd man/create.pedigree.Rd man/gpData2cross.Rd man/kinship.Rd man/plot.genMap.Rd man/Extract.GenMap.Rd man/write.vcf.Rd man/crossVal.Rd man/maize.Rd man/create.gpData.Rd man/simul.phenotype.Rd man/summary.LDdf.Rd man/read.vcf2list.Rd man/plot.LDdf.Rd man/summary.gpData.Rd man/summary.cvData.Rd man/gpData2data.frame.Rd man/predict.gpMod.Rd man/add.gpData.Rd man/simul.pedigree.Rd man/gpMod.Rd man/summary.gpMod.Rd man/write.relationshipMatrix.Rd man/LDMap.Rd man/read.vcf2matrix.Rd man/plot.relationshipMatrix.Rd man/cattle.Rd man/LDDist.Rd man/mice.Rd man/plot.LDmat.Rd man/summary.map.Rd man/discard.individuals.Rd man/discard.markers.Rd man/plot.pedigree.Rd

synbreed documentation built on March 12, 2021, 3:01 a.m.