Intersect a list of bigWig files with a GRanges object (with background)

Intersect a list of bigWig files with a GRanges object and normalize values with a set of background bigWig files.

Usage

.multi_bw_ranges_norm(
  bwfilelist,
  bg_bwfilelist,
  labels,
  granges,
  per_locus_stat = "mean",
  selection = NULL,
  norm_func = identity,
  remove_top = 0,
  default_na = NA_real_,
  scaling = "none"
)

Arguments

bwfilelist

BigWig file list to be summarized.

bg_bwfilelist

Background BigWig files.

labels

List of names to give to the mcols of the returned GRanges object. If NULL, file names are used.

granges

GRanges object to intersect

per_locus_stat

Aggregating function (per locus). Mean by default. Choices: min, max, sd, mean.

selection

A GRanges object to restrict analysis to.

norm_func

Function to apply after bw/bg_bw.

remove_top

Return range 0-(1-remove_top). By default returns the whole distribution (remove_top == 0).

default_na

Default value for missing values

scaling

If none, no operation is performed (default). If relative, values are divided by global mean (1x genome coverage).

Value

a sorted GRanges object