Split fragment file by cell identities

Splits a fragment file into separate files for each group of cells. If splitting multiple fragment files containing common cell types, fragments originating from different files will be appended to the same file for one group of cell identities.

SplitFragments(
  object,
  assay = NULL,
  group.by = NULL,
  idents = NULL,
  outdir = getwd(),
  file.suffix = "",
  append = TRUE,
  buffer_length = 256L,
  verbose = TRUE
)

Arguments

object

A Seurat object

assay

Name of assay to use

group.by

Name of grouping variable to group cells by

idents

List of identities to include

outdir

Directory to write output files

file.suffix

Suffix to add to all file names (before file extension). If splitting multiple fragment files without the append option set to TRUE, an additional numeric suffix will be added to each file (eg, .1, .2).

append

If splitting multiple fragment files, append cells from the same group (eg cluster) to the same file. Note that this can cause the output file to be unsorted.

buffer_length

Size of buffer to be read from the fragment file. This must be longer than the longest line in the file.

verbose

Display messages