methylKit (version 0.9.5)

read.transcript.features: Read transcript features from a BED file

Description

The function returns a GRangesList containing exon, intron, TSS(transcription start site) and promoter locations

Usage

read.transcript.features(location,remove.unsual=TRUE,up.flank=1000,down.flank=1000,unique.prom=TRUE)

Arguments

location

location of the bed file with 12 or more columns

remove.unsual

remove the chromomesomes with unsual names, mainly random chromsomes etc

up.flank

up-stream from TSS to detect promoter boundaries

down.flank

down-stream from TSS to detect promoter boundaries

unique.prom

get only the unique promoters, promoter boundaries will not have a gene name if you set this option to be TRUE

Value

a GRangesList containing locations of exon/intron/promoter/TSS

Examples

# NOT RUN {
gene.obj=read.transcript.features(system.file("extdata", "refseq.hg18.bed.txt", package = "methylKit"))
# }