# chipseq: A package for analyzing chipseq data

## Documentation for package ‘chipseq’ version 1.0.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

as.list-method | A function to read in Aligned Short Reads
basesCovered | Estimate summaries of the distribution of fragment lengths in a
chipseqFilter | Filtering ChIP-seq reads
coerce-method | A function to read in Aligned Short Reads
combineLanes | Combine or subsample short read alignment locations
contextDistribution | Tabulate peak locations according to genomic context
copyIRanges | Associate ranges to coverage.
copyIRangesbyChr | Associate ranges to coverage.
coverageplot | Plot coverage on a small interval.
cstest | A test ChIP-Seq dataset
densityCorr | Estimate summaries of the distribution of fragment lengths in a
diffPeakSummary | A function to identify and produce summary statistics for
diffPeakSummary-method | A function to identify and produce summary statistics for
estimate.mean.fraglen | Estimate summaries of the distribution of fragment lengths in a
estimate.mean.fraglen-method | Estimate summaries of the distribution of fragment lengths in a
extendReads | A function to extend short reads.
islandDepthPlot | Plot island depth distribution
laneSubsample | Combine or subsample short read alignment locations
peakCutoff | Calculate a peak cutoff
peakSummary | Summarizing peak sets
peakSummary-method | Summarizing peak sets
peakSummary-methods | Summarizing peak sets
readReads | A function to read in Aligned Short Reads
sparse.density | Estimate summaries of the distribution of fragment lengths in a
subsetSummary | Compute summaries for cumulative subsets of a short-read data set.