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Calculate profile values of a bigWig file over GRanges object.

Source: R/bwtools.R
dot-calculate_bw_profile.Rd

Calculates profile values of a bigWig file over the loci speficied in a GRanges object. Data points are taken each bin_size base pairs.

Usage

.calculate_bw_profile(
  bw,
  granges,
  bg_bw = NULL,
  label = NULL,
  mode = "stretch",
  bin_size = 100,
  upstream = 2500,
  downstream = 2500,
  middle = NULL,
  ignore_strand = FALSE,
  norm_func = identity,
  remove_top = 0,
  default_na = NA_real_,
  scaling = "none"
)

Arguments

bw

BigWig file to be summarized.

granges

GRanges object

bg_bw

BigWig file to be used as background.

label

Name to give to the values

mode

How to handle differences in lengths across loci:

stretch: Anchor each locus on both sides.

start: Anchor all loci on start.

end: Anchor all loci on end.

center: Center all loci.

bin_size

Bin size. Length of bin in base pairs. The lower, the higher the resolution.

upstream

Number of base pairs to include upstream of loci.

downstream

Number of base pairs to include downstream of loci.

middle

Number of base pairs that the middle section has (in stretch mode). If not provided, median length of all loci is used.

ignore_strand

Whether to use strand information in BED file.

norm_func

Normalization function

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

Whether to use the bigWig values as they are (none - default) or calculate relative enrichment (relative) by dividing values by global average.

Value

A DataFrame with the aggregated scores

Details

Loci are aligned depending on mode parameter:

  • stretch. Aligns all starts and all ends, sort of stretching the loci. The median of these lenghts is taken as the pseudo-length in order to show a realistic plot when displayed.

  • start. All loci are aligned by start.

  • end. All loci are aligned by end.

  • center. All loci are aligned by center.

Adapted from seqplots rtracklayer wrapper functions to compute coverage: For more on seqplots: https://www.bioconductor.org/packages/release/bioc/html/seqplots.html