granges2bed.igv: granges2bed.igv

In demuellae/muRtools: Mueller's R tools

granges2bed.igv

Description

Save a GRanges object to a bed file which can be displayed by IGV

Usage

granges2bed.igv(
  gr,
  fn,
  trackName = NULL,
  scoreCol = NULL,
  na.rm = FALSE,
  nameCol = NULL,
  col.cat = colpal.bde,
  col.cont = c("#EDF8B1", "#41B6C4", "#081D58"),
  col.na = "#bdbdbd",
  col.range = NULL,
  doSort = TRUE
)

Arguments

gr	GRanges object
fn	filename to save bed file to
trackName	track name to be displayed
scoreCol	the score column (in the GRanges elementMetadata) that is optionally used for coloring
na.rm	flag indicating whether items with NA score should be removed
nameCol	the name column (in the GRanges elementMetadata) that is used for labelling the items
col.cat	color panel for coloring categorical scores
col.cont	color panel for coloring numerical scores
col.na	color used for NA scores
col.range	vector of length 2 indicating the range of scores for the color scales to be applied (continuous scores only)
doSort	sort the regions before writing the output

Value

invisibly, the resulting data frame containing the bed file columns

demuellae/muRtools documentation built on Sept. 8, 2023, 4:32 p.m.