SplitFragments function

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