granges2bed: granges2bed

In demuellae/muRtools: Mueller's R tools

granges2bed

Description

Save a GRanges object to a bed file

Usage

granges2bed(
  gr,
  fn,
  score = NULL,
  addAnnotCols = FALSE,
  colNames = FALSE,
  doSort = TRUE,
  bedgraph = FALSE,
  bigBed = FALSE,
  tabix = FALSE,
  strandCharNA = ".",
  coordOnly = FALSE
)

Arguments

gr	GRanges object
fn	filename to save bed file to
addAnnotCols	add the columns stored in elementMetadata of GRanges
colNames	add column names
doSort	sort the regions before writing the output
bedgraph	export to bedgraph instead of bed
bigBed	also save as bigbed file. Requires that the GRanges object has chromosome sizes stored.
tabix	compress and index by tabix
strandCharNA	character to be used if strand is NA, '*' or '.'
coordOnly	output only the coordinates and strand information (only taken into account if addAnnotCols==FALSE). If all strand information is NA, it will be dropped as well.
sc	score vector or column in elementMetadata of GRanges

Value

(invisibly) the written results as a data.frame

demuellae/muRtools documentation built on Nov. 6, 2024, 9:44 a.m.