getGenomicAnnot {transcriptR} | R Documentation

## getGenomicAnnot

### 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)

[Package transcriptR version 1.10.1 Index]