asDGEList               SummarizedExperiment to DGEList
checkBimodality         Check bimodality of regions
clusterFDR              Compute the cluster-level FDR
clusterWindows          Cluster DB windows into clusters
combineOverlaps         Compute overlap statistics
combineTests            Combine statistics across multiple tests
consolidateClusters     Consolidate DB clusters
consolidateSizes        Consolidate window sizes
correlateReads          Compute correlation coefficients between reads
csawUsersGuide          View csaw user's guide
detailRanges            Add annotation to ranges
empiricalFDR            Control the empirical FDR
extractReads            Extract reads from a BAM file
filterWindows           Filtering methods for
                        RangedSummarizedExperiment 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
maximizeCcf             Find the delay at the maximal CCF
mergeWindows            Merge windows into clusters
mixedClusters           Tests for mixed DB clusters
normOffsets             Normalize counts between libraries
profileSites            Profile binding sites
readParam               readParam class and methods
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
