genomation (version 1.4.2)

readTranscriptFeatures: Function for reading exon intron and promoter structure from a given bed file

Description

Function for reading exon intron and promoter structure from a given bed file

Usage

readTranscriptFeatures(location,remove.unusual=TRUE,
                              up.flank=1000,down.flank=1000,unique.prom=TRUE)
## S3 method for class 'character':
readTranscriptFeatures(location, remove.unusual = TRUE,
  up.flank = 1000, down.flank = 1000, unique.prom = TRUE)

Arguments

location

location of the bed file with 12 or more columns. The file can end in .gz, .bz2, .xz, or .zip and/or start with http:// or ftp://. If the file is not compressed it can also start with https:// or ftps://.

remove.unusual

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

my.bed12.file = system.file("extdata/chr21.refseq.hg19.bed", package = "genomation")
my.bed12.file
feats = readTranscriptFeatures(my.bed12.file)
names(feats)
sapply(feats, head)