# ChIP-Seq Analysis with Windows

## Documentation for package ‘csaw’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

$-method | readParam class and methods
asDGEList | SummarizedExperiment to DGEList
asDGEList-method | 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
controlClusterFDR | Compute the cluster-level FDR
correlateReads | Compute correlation coefficients between reads
csaw | View csaw user's guide
csawUsersGuide | View csaw user's guide
detailRanges | Add annotation to ranges
empiricalFDR | Control the empirical FDR
empiricalOverlaps | Compute overlap statistics
extractReads | Extract reads from a BAM file
filterWindows | Filtering methods for RangedSummarizedExperiment objects
findMaxima | Find local maxima
getBestOverlaps | Compute overlap statistics
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
mixedOverlaps | Compute overlap statistics
normalize | Normalize counts between libraries
normalize-method | Normalize counts between libraries
normOffsets | Normalize counts between libraries
normOffsets-method | Normalize counts between libraries
profileSites | Profile binding sites
readParam | readParam class and methods
readParam-class | readParam class and methods
reform | readParam class and methods
reform-method | readParam class and methods
regionCounts | Count reads overlapping each region
scaleControlFilter | Filtering methods for RangedSummarizedExperiment objects
scaledAverage | Scaled average abundance
show-method | readParam class and methods
strandedCounts | Get strand-specific counts
summitOverlaps | Compute overlap statistics
upweightSummit | Upweight summits
windowCounts | Count reads overlapping each window
wwhm | Window width at half maximum