alignPeaks	alignPeaks
alignPeaks,GRanges,character-method	alignPeaks
alignPeaks,GRangesList,ANY-method	alignPeaks
alignPeaks,GRangesList-method	alignPeaks
alignPeaks,IRangesList,list-method	alignPeaks
alignPeaks,list,character-method	alignPeaks
alignPeaks,RangedData,character-method	alignPeaks
alignPeaks-methods	alignPeaks
cmds	cmds
cmds,CompressedGRangesList-method	cmds
cmds,GRangesList-method	cmds
cmds,list-method	cmds
cmds-methods	cmds
cmdsFit	cmdsFit
cmdsFit,matrix-method	cmdsFit
cmdsFit-class	cmdsFit-class
cmdsFit-methods	cmdsFit
countHitsWindow	countHitsWindow
countHitsWindow,GRanges-method	countHitsWindow
countHitsWindow,RangedData-method	countHitsWindow
countHitsWindow-methods	countHitsWindow
coverageDiff	coverageDiff
enrichedChrRegions	enrichedChrRegions
enrichedChrRegions,GRanges,GRanges-method	enrichedChrRegions
enrichedChrRegions,GRanges,missing-method	enrichedChrRegions
enrichedChrRegions,RangedData,missing-method	enrichedChrRegions
enrichedChrRegions,RangedData,RangedData-method	enrichedChrRegions
enrichedChrRegions-methods	enrichedChrRegions
enrichedPeaks	enrichedPeaks
enrichedPeaks,GRanges,GRanges,GRanges-method	enrichedPeaks
enrichedPeaks,GRanges,GRanges,missing-method	enrichedPeaks
enrichedPeaks,GRanges,missing,missing-method	enrichedPeaks
enrichedPeaks,RangedData,IRanges,IRanges-method	enrichedPeaks
enrichedPeaks,RangedData,IRanges,missing-method	enrichedPeaks
enrichedPeaks,RangedData,IRangesList,IRangesList-method	enrichedPeaks
enrichedPeaks,RangedData,IRangesList,missing-method	enrichedPeaks
enrichedPeaks,RangedData,RangedData,missing-method	enrichedPeaks
enrichedPeaks,RangedData,RangedData,RangedData-method	enrichedPeaks
enrichedPeaks-methods	enrichedPeaks
enrichedRegions	enrichedRegions
enrichedRegions,GRanges,GRanges,missing,ANY,ANY-method	enrichedRegions
enrichedRegions,GRanges,missing,missing,ANY,ANY-method	enrichedRegions
enrichedRegions,GRangesList,missing,missing,ANY,ANY-method	enrichedRegions
enrichedRegions,list,missing,missing,ANY,ANY-method	enrichedRegions
enrichedRegions,missing,missing,GRanges,ANY,ANY-method	enrichedRegions
enrichedRegions,missing,missing,RangedData,ANY,missing-method	enrichedRegions
enrichedRegions,missing,missing,RangedData,ANY,numeric-method	enrichedRegions
enrichedRegions,RangedData,missing,missing,ANY,ANY-method	enrichedRegions
enrichedRegions,RangedData,RangedData,missing,ANY,ANY-method	enrichedRegions
enrichedRegions-methods	enrichedRegions
extendRanges	extendRanges
extendRanges,GRanges-method	extendRanges
extendRanges,GRangesList-method	extendRanges
extendRanges,list-method	extendRanges
extendRanges,RangedData-method	extendRanges
extendRanges-methods	extendRanges
fdrEnrichedCounts	fdrEnrichedCounts
filterDuplReads	filterDuplReads
filterDuplReads,GRanges-method	filterDuplReads
filterDuplReads,GRangesList-method	filterDuplReads
filterDuplReads,list-method	filterDuplReads
filterDuplReads,RangedData-method	filterDuplReads
filterDuplReads-methods	filterDuplReads
findPeakHeight	findPeakHeight
findPeakHeight,GRanges,GRanges,GRanges-method	findPeakHeight
findPeakHeight,RangedData,IRangesList,IRangesList-method	findPeakHeight
findPeakHeight,RangedData,RangedData,RangedData-method	findPeakHeight
findPeakHeight,RangedData,Rle,Rle-method	findPeakHeight
findPeakHeight-methods	findPeakHeight
getCover	gridCover-class
getCover,gridCover-method	gridCover-class
getViewsInfo	gridCover-class
getViewsInfo,gridCover-method	gridCover-class
giniCoverage	giniCoverage
giniCoverage,GRanges,ANY,ANY,ANY,character,integer-method	giniCoverage
giniCoverage,GRanges,ANY,ANY,ANY,character,missing-method	giniCoverage
giniCoverage,GRanges,ANY,ANY,ANY,missing,integer-method	giniCoverage
giniCoverage,GRanges,ANY,ANY,ANY,missing,missing-method	giniCoverage
giniCoverage,GRangesList,ANY,ANY,ANY,character,integer-method	giniCoverage
giniCoverage,GRangesList,ANY,ANY,ANY,character,missing-method	giniCoverage
giniCoverage,GRangesList,ANY,ANY,ANY,missing,integer-method	giniCoverage
giniCoverage,GRangesList,ANY,ANY,ANY,missing,missing-method	giniCoverage
giniCoverage,list,ANY,ANY,ANY,character,integer-method	giniCoverage
giniCoverage,list,ANY,ANY,ANY,character,missing-method	giniCoverage
giniCoverage,list,ANY,ANY,ANY,missing,integer-method	giniCoverage
giniCoverage,list,ANY,ANY,ANY,missing,missing-method	giniCoverage
giniCoverage,RangedData,ANY,ANY,ANY,character,integer-method	giniCoverage
giniCoverage,RangedData,ANY,ANY,ANY,character,missing-method	giniCoverage
giniCoverage,RangedData,ANY,ANY,ANY,missing,integer-method	giniCoverage
giniCoverage,RangedData,ANY,ANY,ANY,missing,missing-method	giniCoverage
giniCoverage-methods	giniCoverage
gridCover-class	gridCover-class
gridCoverage	regionsCoverage
htSample	htSample
islandCounts	islandCounts
islandCounts,GRanges-method	islandCounts
islandCounts,GRangesList-method	islandCounts
islandCounts,list-method	islandCounts
islandCounts,RangedData-method	islandCounts
islandCounts-methods	islandCounts
lines,gridCover-method	gridCover-class
listOverlap	listOverlap
listOverlap,character,character,character,character-method	listOverlap
listOverlap,character,character,missing,character-method	listOverlap
listOverlap,factor,character,missing,missing-method	listOverlap
listOverlap-methods	listOverlap
mergeRegions	mergeRegions
mergeRegions,data.frame-method	mergeRegions
mergeRegions,GRanges-method	mergeRegions
mergeRegions,IRanges-method	mergeRegions
mergeRegions,matrix-method	mergeRegions
mergeRegions,RangedData-method	mergeRegions
mergeRegions,RleViews-method	mergeRegions
mergeRegions-methods	mergeRegions
PeakLocation	stdPeakLocation
PeakLocation,data.frame-method	stdPeakLocation
PeakLocation,GRanges-method	stdPeakLocation
PeakLocation,RangedData-method	stdPeakLocation
PeakLocation-methods	stdPeakLocation
plot,cmdsFit,ANY-method	plot-methods
plot,cmdsFit-method	plot-methods
plot,gridCover,ANY-method	gridCover-class
plot,gridCover-method	plot-methods
plotChrRegions	plotChrRegions
plotMeanCoverage	stdPeakLocation
plotMeanCoverage,RleList,RangedData-method	stdPeakLocation
plotMeanCoverage-methods	stdPeakLocation
plotminHeight	findPeakHeight
regionsCoverage	regionsCoverage
regionsCoverage,ANY,ANY,ANY,RleList-method	regionsCoverage
regionsCoverage-methods	regionsCoverage
rowLogRegLRT	rowLogRegLRT
show,gridCover-method	gridCover-class
ssdCoverage	ssdCoverage
ssdCoverage,GRanges-method	ssdCoverage
ssdCoverage,GRangesList-method	ssdCoverage
ssdCoverage,IRangesList-method	ssdCoverage
ssdCoverage,list-method	ssdCoverage
ssdCoverage,RangedData-method	ssdCoverage
ssdCoverage-methods	ssdCoverage
stdGrid	regionsCoverage
stdGrid,gridCover-method	regionsCoverage
stdGrid-methods	regionsCoverage
stdPeakLocation	stdPeakLocation
stdPeakLocation,data.frame-method	stdPeakLocation
stdPeakLocation,GRanges-method	stdPeakLocation
stdPeakLocation,RangedData-method	stdPeakLocation
stdPeakLocation-methods	stdPeakLocation
tabDuplReads	filterDuplReads
tabDuplReads,GRanges-method	filterDuplReads
tabDuplReads,GRangesList-method	filterDuplReads
tabDuplReads,list-method	filterDuplReads
tabDuplReads,RangedData-method	filterDuplReads
tabDuplReads-methods	filterDuplReads
[,gridCover,ANY,ANY,ANY-method	gridCover-class
