FilterCells: Filter cells from fragment file

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

Filter cells from fragment file

Description

Remove all fragments that are not from an allowed set of cell barcodes from the fragment file. This will create a new file on disk that only contains fragments from cells specified in the cells argument. The output file is block gzip-compressed and indexed.

Usage

FilterCells(
  fragments,
  cells,
  outfile = NULL,
  buffer_length = 256L,
  verbose = TRUE
)

Arguments

fragments	Path to a fragment file
cells	A vector of cells to keep
outfile	Name for output file
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

Filter cells from fragment file

Examples

fpath <- system.file("extdata", "fragments.tsv.gz", package="scUtils")
cells <- readLines(system.file("extdata", "cell_name.txt", package="scUtils"))
tmpf <- tempfile(fileext = ".gz")
FilterCells(
  fragments = fpath,
  cells = cells,
  outfile = tmpf
)
file.remove(tmpf)

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