# ChIP-Seq Analysis with Windows

## Documentation for package ‘csaw’ version 1.38.0

- 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
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
combineOverlaps | Combine statistics for overlap-based clusters
combineTests | Combine statistics across multiple tests
consolidateOverlaps | Defunct functions
consolidateTests | Defunct functions
consolidateWindows | Defunct functions
controlClusterFDR | Compute the cluster-level FDR
correlateReads | Compute correlation coefficients between reads
csaw | View csaw user's guide
csawUsersGuide | View csaw user's guide
defunct | Defunct functions
detailRanges | Add annotation to ranges
empiricalFDR | Control the empirical FDR
empiricalOverlaps | Combine statistics for overlap-based clusters
extractReads | Extract reads from a BAM file
filterWindows | Defunct functions
filterWindowsControl | Filtering methods for RangedSummarizedExperiment objects
filterWindowsGlobal | Filtering methods for RangedSummarizedExperiment objects
filterWindowsLocal | Filtering methods for RangedSummarizedExperiment objects
filterWindowsProportion | Filtering methods for RangedSummarizedExperiment objects
findMaxima | Find local maxima
findOverlapsList | Consolidate window sizes
getBestOverlaps | Combine statistics for overlap-based clusters
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
mixedClusters | Tests for mixed DB clusters
mixedOverlaps | Combine statistics for overlap-based clusters
mixedTests | Tests for mixed DB clusters
normFactors | Scaling normalization across libraries
normOffsets | Normalize trended biases across libraries
overlapResults | Wrappers to get region-level results
overlapResultsList | Wrappers to combine multiple analyses
overlapStats | Combine statistics for overlap-based clusters
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 | Combine statistics for overlap-based clusters
upweightSummit | Upweight summits
windowCounts | Count reads overlapping each window
wwhm | Window width at half maximum