getTargetAnnotationStats {genomation} | R Documentation |
This function retrieves percentage/number of target features overlapping with annotation
getTargetAnnotationStats(x,percentage=TRUE,precedence=TRUE) ## S4 method for signature 'AnnotationByFeature' getTargetAnnotationStats(x, percentage = TRUE, precedence = TRUE)
x |
a |
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. |
a vector of percentages or counts showing quantity of target features overlapping with annotation
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)