chipseq: A package for analyzing chipseq data


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Documentation for package ‘chipseq’ version 0.2.1

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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.