getGenomicAnnot-methods: getGenomicAnnot

Description Usage Arguments Details Value Author(s) See Also Examples

Description

Retrieve genomic distribution of ChIP-seq peaks at distinct genomic features (exons, introns, TSSs, intergenic regions)

Usage

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getGenomicAnnot(object)

## S4 method for signature 'ChipDataSet'
getGenomicAnnot(object)

Arguments

object

A ChipDataSet object.

Details

A simple quality check of the supplied ChIP-seq peaks can be performed by investigating their genomic distribution. Ideally, these peaks should demonstrate substantial enrichment at TSS regions. Enrichment of the peaks at a given genomic feature (e.g. TSS) is defined as the ratio between the observed and expected number of peaks. The expected number of peaks is calculated from the proportion of the genome covered by the given genomic feature.

Value

A four column Data.Frame, storing information about observed and expected number of peaks at distinct genomic features.

Author(s)

Armen R. Karapetyan

See Also

constructCDS

Examples

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### Load ChipDataSet object
data(cds)

getGenomicAnnot(cds)


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