as.list,AlignedRead-method	readReads
basesCovered	estimate.mean.fraglen
chipseqFilter	chipseqFilter
coerce,AlignedRead,GenomeData-method	readReads
combineLanes	combineLanes
contextDistribution	contextDistribution
copyIRanges	copyIRangesbyChr
copyIRangesbyChr	copyIRangesbyChr
coverageplot	coverageplot
cstest	cstest
densityCorr	estimate.mean.fraglen
diffPeakSummary	diffPeakSummary
diffPeakSummary,RleViewsList,RleViewsList-method	diffPeakSummary
estimate.mean.fraglen	estimate.mean.fraglen
estimate.mean.fraglen,AlignedRead-method	estimate.mean.fraglen
estimate.mean.fraglen,GenomeData-method	estimate.mean.fraglen
estimate.mean.fraglen,GRanges-method	estimate.mean.fraglen
estimate.mean.fraglen,IntegerList-method	estimate.mean.fraglen
estimate.mean.fraglen,list-method	estimate.mean.fraglen
estimate.mean.fraglen,RangedData-method	estimate.mean.fraglen
estimate.mean.fraglen,RangesList-method	estimate.mean.fraglen
extendReads	extendReads
islandDepthPlot	islandDepthPlot
laneSubsample	combineLanes
peakCutoff	peakCutoff
peakSummary	peakSummary-methods
peakSummary,RleViews-method	peakSummary-methods
peakSummary,RleViewsList-method	peakSummary-methods
peakSummary-methods	peakSummary-methods
readReads	readReads
sparse.density	estimate.mean.fraglen
subsetSummary	subsetSummary
