# chipseq: A package for analyzing chipseq data

## Documentation for package ‘chipseq’ version 0.2.1

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

as.list,AlignedRead-method | A function to read in Aligned Short Reads
basesCovered | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks.
coerce,AlignedRead,GenomeData-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 short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks.
diffPeakSummary | A function to identify and produce summary statistics for differentially expressed peaks.
estimate.mean.fraglen | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks.
estimate.mean.fraglen,AlignedRead-method | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks.
estimate.mean.fraglen,GenomeData-method | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks.
estimate.mean.fraglen,IntegerList-method | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks.
estimate.mean.fraglen,list-method | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks.
estimate.mean.fraglen,RangedData-method | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks.
estimate.mean.fraglen,RangesList-method | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks.
extendReads | A function to extend short reads.
genomic_exons | (Deprecated) Functions that compute genomic regions of interest.
genomic_introns | (Deprecated) Functions that compute genomic regions of interest.
genomic_regions | (Deprecated) Functions that compute genomic regions of interest.
laneSubsample | Combine or subsample short read alignment locations
readReads | A function to read in Aligned Short Reads
sparse.density | Estimate summaries of the distribution of fragment lengths in a short-read experiment. The methods are designed for ChIP-Seq experiments and may not work well in data without peaks.
subsetSummary | Compute summaries for cumulative subsets of a short-read data set.