synbreed: Framework for the Analysis of Genomic Prediction Data using R

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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).

Author
Valentin 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 publication
2016-11-17 16:37:40
Maintainer
Hans-Juergen Auinger <auinger@tum.de>
License
GPL-3
Version
0.11-44
URLs

View on R-Forge

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