Files in rscharpf/VanillaICE
A Hidden Markov Model for high throughput genotyping arrays
.Rbuildignore
.gitignore
CHANGES
DESCRIPTION
NAMESPACE
NEWS
R/AllClasses.R
R/AllGenerics.R
R/datasets.R
R/functions.R
R/help.R
R/hmm-methods.R
R/methods-ArrayViews.R
R/methods-CopyNumScanParams.R
R/methods-EmissionParam.R
R/methods-FilterParam.R
R/methods-HMM.R
R/methods-HMMList.R
R/methods-HmmGRanges.R
R/methods-HmmParam.R
R/methods-HmmTrellisParam.R
R/methods-IdiogramParams.R
R/methods-LogLik.R
R/methods-SnpArrayExperiment.R
R/methods-SnpDataFrame.R
R/methods-TransitionParam.R
R/methods-Viterbi.R
R/updates.R
R/zzz.R
changelog
data/snp_exp.rda
inst/CITATION
inst/NEWS.Rd
inst/extdata/FinalReport1664.txt
inst/extdata/FinalReport1675.txt
inst/extdata/FinalReport1686.txt
inst/extdata/FinalReport6841.txt
inst/extdata/FinalReport6872.txt
inst/extdata/FinalReport6903.txt
inst/extdata/SNP_info.csv
inst/extdata/sample_data.csv
inst/extdata/snp_exp.rda
inst/illumina/illuminaEx.txt
inst/scripts/crlmmDownstream.Rnw
inst/scripts/crlmmDownstream.pdf
inst/scripts/runcrlmm.R
inst/test/crlmmDownstream.Rnw
inst/unitTests/Makefile
inst/unitTests/TestData.R
inst/unitTests/test_ArrayViews.R
inst/unitTests/test_BeadStudioSet.R
inst/unitTests/test_FilterParam.R
inst/unitTests/test_HmmGRanges.R
inst/unitTests/test_HmmParam.R
inst/unitTests/test_SnpArrayExperiment.R
inst/unitTests/test_SnpGRanges.R
inst/unitTests/test_SummarizedExperiment.R
inst/unitTests/test_acf2.R
inst/unitTests/test_constraints.R
inst/unitTests/test_hmm.R
inst/unitTests/test_loess.R
inst/unitTests/test_oligoSetList.R
inst/unitTests/test_rowMAD.R
inst/unitTests/test_scaleBy.R
inst/unitTests/test_sweepMode.R
inst/unitTests/test_viterbi.R
man/ArrayViews-class.Rd
man/CopyNumScanParams.Rd
man/EmissionParam-methods.Rd
man/FilterParam-class.Rd
man/HMM.Rd
man/HMMList-class.Rd
man/HMMList.Rd
man/HmmGRanges-methods.Rd
man/HmmParam.Rd
man/HmmTrellisParam.Rd
man/IO.Rd
man/IdiogramParam-class.Rd
man/IdiogramParams-class.Rd
man/LogLik-class.Rd
man/LogLik.Rd
man/LowLevelSummaries.Rd
man/NA_filter.Rd
man/SnpArrayExperiment-class.Rd
man/SnpExperiment.Rd
man/SnpGRanges.Rd
man/TransitionParam.Rd
man/VanillaICE.Rd
man/Viterbi-methods.Rd
man/acf2.Rd
man/baumWelchUpdate.Rd
man/calculateEmission.Rd
man/cnvFilter.Rd
man/doUpdate.Rd
man/dropDuplicatedMapLocs.Rd
man/dropSexChrom.Rd
man/emission.Rd
man/emissionParam.Rd
man/filters.Rd
man/getExampleSnpExperiment.Rd
man/getHmmParams.Rd
man/hmm2.Rd
man/hmmResults.Rd
man/isHeterozygous.Rd
man/matrixOrNULL-class.Rd
man/numberFeatures.Rd
man/parseSourceFile.Rd
man/parsedPath.Rd
man/plotting.Rd
man/probability.Rd
man/rescale.Rd
man/robust-statistics.Rd
man/segs.Rd
man/snpArrayAssays.Rd
man/snp_exp.Rd
man/sourcePaths.Rd
man/start-oligoSnpSet-method.Rd
man/state-methods.Rd
man/sweepMode.Rd
man/threshold.Rd
man/updateHmmParams.Rd
man/viewports.Rd
src/Makevars
src/rinit.c
src/viterbi.c
tests/doRUnit.R
vignettes/VanillaICE.Rnw
vignettes/crlmmDownstream.Rnw
vignettes/ice.bib
