genomation (version 1.4.2)

getAssociationWithTSS: Get distance to nearest TSS and gene id from AnnotationByGeneParts

Description

This accessor function gets the nearest TSS, its distance to target feature, strand and name of TSS/gene from AnnotationByGeneParts object

Usage

getAssociationWithTSS(x)
## S3 method for class 'AnnotationByGeneParts':
getAssociationWithTSS(x)

Arguments

x

a AnnotationByGeneParts object

Value

• RETURNS a data.frame containing row number of the target features, distance of target to nearest TSS, TSS/Gene name, TSS strand

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)
head(getAssociationWithTSS(cage.annot))