bed_to_granges: Read bedfile into GRanges

In multicrispr: Multi-locus multi-purpose Crispr/Cas design

Description

Read bedfile into GRanges

Usage

bed_to_granges(
  bedfile,
  genome,
  txdb = NULL,
  do_order = TRUE,
  plot = TRUE,
  verbose = TRUE
)

Arguments

bedfile	file path
genome	string: UCSC genome name (e.g. 'mm10')
txdb	NULL (default) or TxDb-class (used for gene annotation)
do_order	TRUE (default) or FALSE: order on seqnames and star?
plot	TRUE (default) or FALSE: plot karyogram?
verbose	TRUE (default) or FALSE

Value

GRanges-class

See Also

char_to_granges, genes_to_granges

Examples

bedfile  <- system.file('extdata/SRF.bed', package = 'multicrispr')
bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
(gr <- bed_to_granges(bedfile, genome='mm10'))

multicrispr documentation built on Nov. 8, 2020, 5:10 p.m.