asDGEList               SummarizedExperiment to DGEList
calculateCPM            Calculate CPM
checkBimodality         Check bimodality of regions
cluster-direction       Reporting cluster-level direction in 'csaw'
clusterFDR              Compute the cluster-level FDR
clusterWindows          Cluster DB windows into clusters
clusterWindowsList      Consolidate DB clusters
combineTests            Combine statistics across multiple tests
correlateReads          Compute correlation coefficients between reads
csawUsersGuide          View csaw user's guide
defunct                 Defunct functions
detailRanges            Add annotation to ranges
empiricalFDR            Control the empirical FDR
extractReads            Extract reads from a BAM file
filterWindowsProportion
                        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
mergeResults            Wrappers to get region-level results
mergeResultsList        Wrappers to combine multiple analyses
mergeWindows            Merge windows into clusters
mergeWindowsList        Consolidate window sizes
minimalTests            Require rejection of a minimal number of tests
mixedTests              Tests for mixed DB clusters
normFactors             Scaling normalization across libraries
normOffsets             Normalize trended biases across libraries
overlapStats            Combine statistics for overlap-based clusters
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
