Files in vsbuffalo/ProgenyArray
Some statistical genetics for progeny array experiments
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/AllClasses.R
R/AllGenerics.R
R/ProgenyArray-package.r
R/RcppExports.R
R/haplotype-simulation.R
R/parentage-methods.R
R/phasing-output.R
R/phasing-plots.R
R/phasing-utilities.R
R/phasing.R
R/progenyarray-methods.R
R/sim.R
R/simulation-methods.R
R/tile-methods.R
R/utilities.R
README.md
man/HW.Rd
man/HWPlot.Rd
man/MendelianTransmissionWithError.Rd
man/PhasingTiles-class.Rd
man/ProgenyArray-class.Rd
man/ProgenyArray.Rd
man/SimulatedProgenyArray-class.Rd
man/SimulatedProgenyArray.Rd
man/allSibFamilies.Rd
man/alleleFreqs.Rd
man/approxGeneticMap.Rd
man/caclulateLODs.Rd
man/calcFreqs-ProgenyArray-method.Rd
man/calcFreqs.Rd
man/emHaplotypeImpute.Rd
man/emPlot.Rd
man/extractProgenyHaplotypes.Rd
man/fathers-ProgenyArray-method.Rd
man/fathers-set.Rd
man/fathers.Rd
man/filterSibFamilies.Rd
man/freqs-ProgenyArray-method.Rd
man/freqs-set.Rd
man/freqs.Rd
man/geneticTiles.Rd
man/genotypeFreqs.Rd
man/genotypingErrorMatrix.Rd
man/granges-ProgenyArray-method.Rd
man/hapAgreementStats.Rd
man/inferParents-ProgenyArray-method.Rd
man/inferParents-SimulatedProgenyArray-method.Rd
man/inferParents.Rd
man/isSelfed-ProgenyArray-method.Rd
man/isSelfed.Rd
man/loadGeneticMap.Rd
man/lodcutoff-set.Rd
man/lodcutoff.Rd
man/miMatrixPerTile.Rd
man/miRates.Rd
man/mothers-ProgenyArray-method.Rd
man/mothers-set.Rd
man/mothers.Rd
man/parentGenotypes-ProgenyArray-method.Rd
man/parentGenotypes-SimulatedProgenyArray-method.Rd
man/parentGenotypes.Rd
man/parentLLPlot-ProgenyArray-method.Rd
man/parentLLPlot.Rd
man/parentNames-ProgenyArray-method.Rd
man/parentNames-set.Rd
man/parentNames.Rd
man/parentage.Rd
man/parents-ProgenyArray-method.Rd
man/parents.Rd
man/phaseParents-ProgenyArray-method.Rd
man/phaseParents.Rd
man/phaseSibFamily.Rd
man/phases-ProgenyArray-method.Rd
man/phases.Rd
man/physicalTiles.Rd
man/plotGeneticMap.Rd
man/predictGeneticMap.Rd
man/progenyArray-SimulatedProgenyArray-method.Rd
man/progenyGenotypes-ProgenyArray-method.Rd
man/progenyGenotypes-SimulatedProgenyArray-method.Rd
man/progenyGenotypes.Rd
man/progenyNames-ProgenyArray-method.Rd
man/progenyNames-set.Rd
man/progenyNames.Rd
man/show-PhasingTiles-method.Rd
man/show-ProgenyArray-method.Rd
man/sibFamily.Rd
man/snpTiles.Rd
man/suppliedMothers-ProgenyArray-method.Rd
man/suppliedMothers-set.Rd
man/suppliedMothers.Rd
man/tileRef.Rd
man/whichLociComplete.Rd
man/whichLociPolymorphic.Rd
man/whichRowColMax.Rd
src/Makevars
src/RcppExports.cpp
src/genealogy.cpp
src/methods.cpp
src/models.cpp
src/models.h
src/phasing.cpp
tests/testthat.R
tests/testthat/test-parentage.R
vignettes/em-phasing.Rmd
vignettes/graphmodel.dot
vignettes/ibds.Rmd
vignettes/methods.bib
vignettes/methods.tex
vignettes/parent-imput.dot
vignettes/phasing.Rmd
