methylKit (version 0.99.2)

readTranscriptFeatures: Read transcript features from a BED file

Description

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

Usage

readTranscriptFeatures(location, remove.unsual = TRUE, up.flank = 1000,
  down.flank = 1000, unique.prom = TRUE)
# S4 method for character
readTranscriptFeatures(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 chromosomes with unsual names, mainly random chromosomes 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=readTranscriptFeatures(system.file("extdata", 
"refseq.hg18.bed.txt", package = "methylKit"))

# }