SplitFragments: Split fragment file by cell identities

In wzthu/ATACpipe: An Easy-to-use Systematic pipeline for ATACseq data analysis

Split fragment file by cell identities

Description

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.

Usage

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

Value

SplitFragments

wzthu/ATACpipe documentation built on Aug. 12, 2022, 7:38 a.m.