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

Global functions
.adapGridMosaicsZ0_IO Man page
.adapGridMosaicsZ0_OS Man page
.adapGridMosaicsZ0_TS Man page
.calMDZ1_2S Man page
.calcModelBIC Man page
.calcPN Man page
.computeStat Man page
.eStepZ1_2S Man page
.emZ1_2S Man page
.exportBED Man page
.exportGFF Man page
.exportTXT Man page
.getPH_1S Man page
.getPH_2S Man page
.getParamZ0 Man page
.getPi0 Man page
.mStepZ1_2S Man page
.margDistZ1_1S Man page
.margDistZ1_2S Man page
.margDist_1S Man page
.margDist_2S Man page
.mosaicsFit_IO Man page
.mosaicsFit_OS Man page
.mosaicsFit_TS Man page
.mosaicsZ0_IO Man page
.mosaicsZ0_OS Man page
.mosaicsZ0_TS Man page
.mosaicsZ1_1S Man page
.mosaicsZ1_2S Man page
.peakCall Man page
.plotGOF Man page
.processBin_MGC Man page
.processBin_MGCX Man page
.processBin_X Man page
.reportSummary Man page
.rlmFit_IO Man page
.rlmFit_OS Man page
.rlmFit_TS Man page
.validDataType Man page
.validLocation Man page
.validType Man page
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
adapGridMosaicsZ0_IO Source code
adapGridMosaicsZ0_OS Source code
adapGridMosaicsZ0_TS Source code
adjustBoundary Man page
adjustBoundary,MosaicsPeak-method Man page
annotateHMM Source code
annotatePeak Source code
bdBin Man page
bdBin,MosaicsPeak-method Man page
calMDZ1_2S Source code
calcModelBIC Source code
calcPN Source code
calcYbdAll Source code
chrID Man page
chrID,BinData-method Man page
computeStat Source code
constructBins Man page Source code
constructExtRead Source code
conv_1S Man page Source code
conv_2S Man page Source code
coord Man page
coord,BinData-method Man page
eStepZ1_2S Source code
emZ1_2S Source code
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
exportBED Source code
exportEncodePeak Source code
exportGFF Source code
exportTXT Source code
extractPostProb Source code
extractReads Man page
extractReads,MosaicsPeak-method Man page
extread2GRanges Source code
ff_emHMM Source code
ff_stack Source code
ff_updatePiMat Source code
ff_viterbi Source code
filterPeak Man page
filterPeak,MosaicsPeak-method Man page
findSummit Man page
findSummit,MosaicsPeak-method Man page
fitHMM Source code
gcContent Man page
gcContent,BinData-method Man page
generateWig Man page Source code
getPH_1S Source code
getPH_2S Source code
getParamZ0 Source code
getPi0 Source code
input Man page
input,BinData-method Man page
loadReadData Source code
logLik Source code
mStepZ1_2S Source code
mappability Man page
mappability,BinData-method Man page
margDistZ1_1S Source code
margDistZ1_2S Source code
margDist_1S Source code
margDist_2S Source code
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
mosaicsFit_IO Source code
mosaicsFit_OS Source code
mosaicsFit_TS Source code
mosaicsPeak Man page
mosaicsPeak,MosaicsFit-method Man page
mosaicsPeakHMM Man page
mosaicsPeakHMM,MosaicsHMM-method Man page
mosaicsRunAll Man page Source code
mosaicsZ0 Source code
mosaicsZ1_1S Source code
mosaicsZ1_2S Source code
peakCall 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
plotGOF Source code
plotGOFHMM Source code
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
processBin_MGC Source code
processBin_MGCX Source code
processBin_X Source code
processBin_XN Source code
read Man page
read,MosaicsPeak-method Man page
readBins Man page Source code
readCoverage Man page
readCoverage,MosaicsPeak-method Man page
reportSummary Source code
rlmFit_IO Source code
rlmFit_OS Source code
rlmFit_TS Source code
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
simulateHMM_1S Source code
simulateHMM_2S Source code
tagCount Man page
tagCount,BinData-method Man page
trimExtend Source code
validDataType Source code
validLocation Source code
validType Source code
mosaics documentation built on May 31, 2017, 3:09 p.m.