genomation (version 1.4.2)

getTargetAnnotationStats: 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)
## S3 method for class '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)