getGenomicAnnot-methods: getGenomicAnnot

In transcriptR: An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification

Description

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

Usage

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

### Load ChipDataSet object
data(cds)

getGenomicAnnot(cds)

transcriptR documentation built on Nov. 8, 2020, 8:12 p.m.