Files in mosaics

MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)

R/base_rlmFit_IO.R R/base_calcYbdAll.R R/base_peakCall.R R/base_plotGOFHMM.R R/base_margDist_2S.R R/base_annotateHMM.R R/base_mosaicsZ0.R R/base_mosaicsZ1_2S.R R/base_computeStat.R R/base_convolution_1S_cpp.R R/base_fitHMM.R R/base_adapGridMosaicsZ0_IO.R R/AllGenerics.R R/methods_MosaicsFit.R R/base_mosaicsZ1_1S.R R/base_calcPN.R R/base_logLik.R R/mosaicsFitHMM.R R/filterPeak.R R/adjustBoundary.R R/findSummit.R R/base_calcModelBIC.R R/mosaicsPeak.R R/base_getPi0.R R/base_margDist_1S.R R/base_extractPostProb.R R/base_getParamZ0.R R/base_reportSummary.R R/constructBins.R R/extractReads.R R/base_adapGridMosaicsZ0_TS.R R/mosaicsRunAll.R R/mosaicsPeakHMM.R R/generateWig.R R/base_trimExtend.R R/readBins.R R/AllClasses.R R/base_rlmFit_OS.R R/base_loadReadData.R R/base_annotatePeak.R R/mosaicsFit.R R/base_export.R R/base_convolution_2S_cpp.R R/methods_MosaicsHMM.R R/base_rlmFit_TS.R R/methods_BinData.R R/base_cpp_call.R R/base_plotGOF.R R/base_adapGridMosaicsZ0_OS.R R/base_constructExtRead.R R/methods_MosaicsPeak.R vignettes/Figure4a.pdf vignettes/GOF_matchLow.pdf vignettes/Figure4b.pdf vignettes/Figure5b.pdf vignettes/GOF_rMOM.pdf vignettes/Figure5c.pdf vignettes/Figure5d.pdf vignettes/igv.pdf vignettes/Figure5a.pdf man/estimates.Rd man/MosaicsPeak-class.Rd man/mosaics-internal.Rd man/extractReads.Rd man/readBins.Rd man/fllterPeak.Rd man/findSummit.Rd man/MosaicsPeakParam-class.Rd man/MosaicsFit-class.Rd man/mosaicsFitHMM.Rd man/BinData-class.Rd man/constructBins.Rd man/mosaicsPeakHMM.Rd man/export.Rd man/mosaicsRunAll.Rd man/mosaicsFit.Rd man/TagData-class.Rd man/generateWig.Rd man/MosaicsHMM-class.Rd man/MosaicsFitParam-class.Rd man/adjustBoundary.Rd man/MosaicsFitEst-class.Rd man/mosaics-package.Rd man/mosaicsPeak.Rd inst/doc/mosaics-example.pdf inst/doc/mosaics-example.R