# ChIP-seq analysis with windows

## Documentation for package ‘csaw’ version 1.0.7

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

## Help Pages

$-method | readParam class and methods
asDGEList | Statistical wrappers for SummarizedExperiment objects
asDGEList-method | Statistical wrappers for SummarizedExperiment objects
average | Statistical wrappers for SummarizedExperiment objects
average-method | Statistical wrappers for SummarizedExperiment objects
combineTests | Combine statistics across multiple tests
correlateReads | Compute correlation coefficients between reads
csawUsersGuide | View csaw user's guide
detailRanges | Add annotation to ranges
extractReads | Extract reads from a BAM file
getBestTest | Get the best test in a cluster
getPETSizes | Compute fragment lengths for paired-end tags
mergeWindows | Merge windows into clusters
normalize | Statistical wrappers for SummarizedExperiment objects
normalize-method | Statistical wrappers for SummarizedExperiment objects
normalizeCounts | Normalize counts between libraries
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
show-method | readParam class and methods
windowCounts | Count reads overlapping each window