getFeatsWithTargetsStats {genomation} | R Documentation |
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.
getFeatsWithTargetsStats(x,percentage=TRUE) ## S4 method for signature 'AnnotationByFeature' getFeatsWithTargetsStats(x, percentage = TRUE)
x |
a |
percentage |
TRUE|FALSE. If TRUE percentage of annotation features will be returned. If FALSE, number of annotation features will be returned |
RETURNS a vector of percentages or counts showing quantity of annotation features overlapping with target features
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)