AnnotationByGeneParts-methods: Get distance to nearest TSS and gene id from...

Description Usage Arguments Value Examples

Description

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

Usage

1
2
3
4
getAssociationWithTSS(x)

## S4 method for signature '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

1
2
3
4
5
6
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))
 

BIMSBbioinfo/genomation documentation built on Feb. 4, 2018, 12:11 p.m.