getTargetAnnotationStats {genomation} | R Documentation

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

### Description

This function retrieves percentage/number of target features overlapping with annotation

### Usage

    getTargetAnnotationStats(x,percentage=TRUE,precedence=TRUE)

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

### Arguments

`x` | a `AnnotationByFeature` object
`percentage` | TRUE|FALSE. If TRUE percentage of target features will be returned. If FALSE, number of target features will be returned
`precedence` | TRUE|FALSE. If TRUE there will be a hierachy of annotation features when calculating numbers (with promoter>exon>intron precedence) That means if a feature overlaps with a promoter it will be counted as promoter overlapping only, or if it is overlapping with a an exon but not a promoter, #' it will be counted as exon overlapping only whether or not it overlaps with an intron.

### Value

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

### 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)
    getTargetAnnotationStats(cage.annot)

[Package genomation version 1.20.0 Index]