combineOverlaps         Compute overlap statistics
combineTests            Combine statistics across multiple tests
consolidateSizes        Consolidate window sizes
correlateReads          Compute correlation coefficients between reads
csawUsersGuide          View csaw user's guide
detailRanges            Add annotation to ranges
dumpPE                  Dump paired-end data to file
extractReads            Extract reads from a BAM file
filterWindows           Filtering methods for SummarizedExperiment
                        objects
findMaxima              Find local maxima
getBestTest             Get the best test in a cluster
getPESizes              Compute fragment lengths for paired-end tags
getWidths               Get region widths
makeExtVector           Make an extVector object
mergeWindows            Merge windows into clusters
normalize,SummarizedExperiment-method
                        Statistical wrappers for SummarizedExperiment
                        objects
normalizeCounts         Normalize counts between libraries
profileSites            Profile binding sites
readParam               readParam class and methods
reformList              Get or modify readParam lists
regionCounts            Count reads overlapping each region
scaledAverage           Scaled average abundance
strandedCounts          Get strand-specific counts
upweightSummit          Upweight summits
windowCounts            Count reads overlapping each window
wwhm                    Window width at half maximum
