read_bed.Rd
Read bedfile as data.table
read_bed(bedfile, bsgenome, verbose = TRUE, rm_duplicates = TRUE)
bedfile | file path |
---|---|
bsgenome | BSgenome, e.g. BSgenome.Mmusculus.UCSC.mm10::Mmusculus |
verbose | logical(1) |
rm_duplicates | logical(1) |
data.table(chr, start, end, strand)
bedfile <- system.file('extdata/SRF_sites.bed', package = 'multicrispr') bsgenome <- BSgenome.Mmusculus.UCSC.mm10::Mmusculus read_bed(bedfile, bsgenome)#>#>#>#>#> GRanges object with 1974 ranges and 0 metadata columns: #> seqnames ranges strand #> <Rle> <IRanges> <Rle> #> [1] chr1 4712627-4712643 - #> [2] chr1 5250211-5250227 - #> [3] chr1 5250451-5250467 - #> [4] chr1 5256192-5256208 - #> [5] chr1 5985727-5985743 - #> ... ... ... ... #> [1970] chrY 6770311-6770327 + #> [1971] chrY 23130567-23130583 + #> [1972] chrY 42512399-42512415 - #> [1973] chrY 79048175-79048191 - #> [1974] chrY 89126493-89126509 - #> ------- #> seqinfo: 66 sequences (1 circular) from mm10 genome