Calculate a normalized heatmap matrix for a bigWig file over a BED file

Calculate a normalized heatmap matrix for a bigWig file over a BED file

Usage

.calculate_matrix_norm(
  bw,
  granges,
  bg_bw = 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.

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

Summary matrix