chipseq: A package for analyzing chipseq data

Documentation for package ‘chipseq’ version 1.0.0

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.