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/

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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

Files in this package

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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