getFeatsWithTargetsStats {genomation} | R Documentation

## Get the percentage/count of annotation features overlapping with target features from AnnotationByFeature

### Description

This function retrieves percentage/number of annotation features overlapping with targets. For example, if `AnnotationByFeature` object is containing statistics of differentially methylated regions overlapping with gene annotation. This function will return number/percentage of introns,exons and promoters overlapping with differentially methylated regions.

### Usage

    getFeatsWithTargetsStats(x,percentage=TRUE)

    ## S4 method for signature 'AnnotationByFeature'
    getFeatsWithTargetsStats(x, percentage = TRUE)

### Arguments

`x` | a `AnnotationByFeature` object
`percentage` | TRUE|FALSE. If TRUE percentage of annotation features will be returned. If FALSE, number of annotation features will be returned

### Value

RETURNS a vector of percentages or counts showing quantity of annotation features overlapping with target features

### Examples

    data(cage)
    bed.file=system.file("extdata/chr21.refseq.hg19.bed", package = "genomation")
    gene.parts = readTranscriptFeatures(bed.file)
    cage.annot = annotateWithGeneParts(cage, gene.parts, intersect.chr=TRUE)
    getFeatsWithTargetsStats(cage.annot)

[Package genomation version 1.12.0 Index]