R: Load bed file as GRanges.

fread.bed {ORFik}

R Documentation

Load bed file as GRanges.

Description

Wraps around rtracklayer::import.bed and tries to speed up loading with the use of data.table. Supports gzip, gz, bgz and bed formats. Also safer chromosome naming with the argument chrStyle

Usage

fread.bed(filePath, chrStyle = NULL)

Arguments

`filePath`	The location of the bed file
`chrStyle`	a GRanges object, or a `seqlevelsStyle` (Default: NULL) to get seqlevelsStyle from. Is chromosome 1 called chr1 or 1, is mitocondrial chromosome called MT or chrM etc. Will use 1st seqlevel-style if more are present. Like: c("NCBI", "UCSC") -> pick "NCBI"

Value

a GRanges object

Examples

# path to example CageSeq data from hg19 heart sample
cageData <- system.file("extdata", "cage-seq-heart.bed.bgz",
                        package = "ORFik")
fread.bed(cageData)