Write insertion counts to bedgraph file

Write insertion counts data for one or more pseudobulks to bedgraph format. This reports the total number insertions at each basepair for each group listed in cell_groups.

Usage

write_insertion_bedgraph(
  fragments,
  path,
  cell_groups = rlang::rep_along(cellNames(fragments), "all"),
  insertion_mode = c("both", "start_only", "end_only")
)

Arguments

fragments

IterableFragments object

path

(character vector) Path(s) to save bedgraph to, optionally ending in ".gz" to add gzip compression. If cell_groups is provided, path must be a named character vector, with one name for each level in cell_groups

cell_groups

Character or factor assigning a group to each cell, in order of cellNames(fragments)

insertion_mode

(string) Which fragment ends to use for coverage calculation. One of "both", "start_only", or "end_only"