methylKit (version 0.99.2)

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

Description

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

Usage

getAssociationWithTSS(x)
# S4 method for annotationByGenicParts
getAssociationWithTSS(x)

Arguments

x

an annotationByGenicParts object

Value

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

Examples

# NOT RUN {
data(methylKit)
gene.obj=readTranscriptFeatures(system.file("extdata", 
"refseq.hg18.bed.txt", package = "methylKit"))
ann=annotateWithGenicParts(methylDiff.obj, gene.obj)
df=getAssociationWithTSS(ann)
head(df)

# }