API for dongjunchung/mosaics
MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
| Global functions | |
|---|---|
| .adapGridMosaicsZ0_IO | Man page Source code |
| .adapGridMosaicsZ0_OS | Man page Source code |
| .adapGridMosaicsZ0_TS | Man page Source code |
| .annotateHMM | Source code |
| .annotatePeak | Source code |
| .calMDZ1_2S | Man page Source code |
| .calcModelBIC | Man page Source code |
| .calcPN | Man page Source code |
| .calcYbdAll | Source code |
| .computeStat | Man page Source code |
| .constructExtRead | Source code |
| .eStepZ1_2S | Man page Source code |
| .emZ1_2S | Man page Source code |
| .exportBED | Man page Source code |
| .exportEncodePeak | Source code |
| .exportGFF | Man page Source code |
| .exportTXT | Man page Source code |
| .extractPostProb | Source code |
| .extread2GRanges | Source code |
| .ff_emHMM | Source code |
| .ff_stack | Source code |
| .ff_updatePiMat | Source code |
| .ff_viterbi | Source code |
| .fitHMM | Source code |
| .getPH_1S | Man page Source code |
| .getPH_2S | Man page Source code |
| .getParamZ0 | Man page Source code |
| .getPi0 | Man page Source code |
| .loadReadData | Source code |
| .logLik | Source code |
| .mStepZ1_2S | Man page Source code |
| .margDistZ1_1S | Man page Source code |
| .margDistZ1_2S | Man page Source code |
| .margDist_1S | Man page Source code |
| .margDist_2S | Man page Source code |
| .mosaicsFit_IO | Man page Source code |
| .mosaicsFit_OS | Man page Source code |
| .mosaicsFit_TS | Man page Source code |
| .mosaicsZ0 | Source code |
| .mosaicsZ0_IO | Man page |
| .mosaicsZ0_OS | Man page |
| .mosaicsZ0_TS | Man page |
| .mosaicsZ1_1S | Man page Source code |
| .mosaicsZ1_2S | Man page Source code |
| .peakCall | Man page Source code |
| .plotGOF | Man page Source code |
| .plotGOFHMM | Source code |
| .processBin_MGC | Man page Source code |
| .processBin_MGCX | Man page Source code |
| .processBin_X | Man page Source code |
| .processBin_XN | Source code |
| .reportSummary | Man page Source code |
| .rlmFit_IO | Man page Source code |
| .rlmFit_OS | Man page Source code |
| .rlmFit_TS | Man page Source code |
| .simulateHMM_1S | Source code |
| .simulateHMM_2S | Source code |
| .trimExtend | Source code |
| .validDataType | Man page Source code |
| .validLocation | Man page Source code |
| .validType | Man page Source code |
| BinData-class | Man page |
| MosaicsFit-class | Man page |
| MosaicsFitEst-class | Man page |
| MosaicsFitParam-class | Man page |
| MosaicsHMM-class | Man page |
| MosaicsPeak-class | Man page |
| MosaicsPeakParam-class | Man page |
| TagData-class | Man page |
| adjustBoundary | Man page |
| adjustBoundary,MosaicsPeak-method | Man page |
| bdBin | Man page |
| bdBin,MosaicsPeak-method | Man page |
| chrID | Man page |
| chrID,BinData-method | Man page |
| constructBins | Man page Source code |
| conv_1S | Man page Source code |
| conv_2S | Man page Source code |
| coord | Man page |
| coord,BinData-method | Man page |
| empFDR | Man page |
| empFDR,MosaicsPeak-method | Man page |
| estimates | Man page |
| estimates,MosaicsFit-method | Man page |
| estimates,MosaicsHMM-method | Man page |
| export | Man page |
| export,MosaicsPeak-method | Man page Man page |
| extractReads | Man page |
| extractReads,MosaicsPeak-method | Man page |
| filterPeak | Man page |
| filterPeak,MosaicsPeak-method | Man page |
| findSummit | Man page |
| findSummit,MosaicsPeak-method | Man page |
| gcContent | Man page |
| gcContent,BinData-method | Man page |
| generateWig | Man page Source code |
| input | Man page |
| input,BinData-method | Man page |
| mappability | Man page |
| mappability,BinData-method | Man page |
| mosaics | Man page |
| mosaics-package | Man page |
| mosaicsFit | Man page |
| mosaicsFit,BinData-method | Man page Man page |
| mosaicsFitHMM | Man page |
| mosaicsFitHMM,MosaicsFit-method | Man page |
| mosaicsPeak | Man page |
| mosaicsPeak,MosaicsFit-method | Man page |
| mosaicsPeakHMM | Man page |
| mosaicsPeakHMM,MosaicsHMM-method | Man page |
| mosaicsRunAll | Man page Source code |
| plot,BinData,missing-method | Man page |
| plot,MosaicsFit,ANY-method | Man page |
| plot,MosaicsHMM,missing-method | Man page |
| plot,MosaicsPeak,missing-method | Man page |
| postProb | Man page |
| postProb,MosaicsPeak-method | Man page |
| print,BinData-method | Man page |
| print,MosaicsFit-method | Man page |
| print,MosaicsHMM-method | Man page |
| print,MosaicsPeak-method | Man page |
| read | Man page |
| read,MosaicsPeak-method | Man page |
| readBins | Man page Source code |
| readCoverage | Man page |
| readCoverage,MosaicsPeak-method | Man page |
| seqDepth | Man page |
| seqDepth,BinData-method | Man page |
| seqDepth,MosaicsFit-method | Man page |
| seqDepth,MosaicsHMM-method | Man page |
| seqDepth,MosaicsPeak-method | Man page |
| show,BinData-method | Man page |
| show,MosaicsFit-method | Man page |
| show,MosaicsHMM-method | Man page |
| show,MosaicsPeak-method | Man page |
| tagCount | Man page |
| tagCount,BinData-method | Man page |
