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

In fortunatobianconi/methylkit: DNA methylation analysis from high-throughput bisulfite sequencing results

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

Note

one bed track per file is only accepted, the bed files with multiple tracks will cause en error

Examples

gene.obj=read.transcript.features(system.file("extdata", "refseq.hg18.bed.txt", package = "methylKit"))

fortunatobianconi/methylkit documentation built on May 16, 2019, 1:51 p.m.