Files in rscharpf/VanillaICE

A Hidden Markov Model for high throughput genotyping arrays

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 inst/scripts/crlmmDownstream.pdf inst/scripts/runcrlmm.R 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 tests/doRUnit.R