chipseq: A package for analyzing chipseq data

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Documentation for package ‘chipseq’ version 1.2.0

Help Pages

as.list-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.
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 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.
diffPeakSummary-method 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-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.
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 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.