fread.bed: Load bed file as GRanges

In ORFik: Open Reading Frames in Genomics

Description

Wraps around 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, TxDb, FaFile, 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

See Also

Other utils: bedToGR(), convertToOneBasedRanges(), export.bed12(), export.wiggle(), fimport(), findFa(), optimizeReads(), readBam(), readWig()

Examples

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

ORFik documentation built on March 27, 2021, 6 p.m.