Calculate matrix for stretch mode
Usage
.calculate_stretch_matrix(
bw,
granges,
bin_size = 100,
upstream = 2500,
downstream = 2500,
middle = NULL,
ignore_strand = FALSE,
default_na = NA_real_,
scaling = "none"
)Arguments
- bw
BigWigFile object
- granges
GRanges object
- bin_size
Bin size
- upstream
Number of basepairs upstream
- downstream
Number of basepairs downstream
- middle
Number of base pairs that the middle section has. If not provided, median is used.
- ignore_strand
Ignore strand (bool)
- default_na
Default value for missing values
- scaling
none if no scaling is performed (default), relative if 1x scaling is done (divide by global coverage).