Filter cells from fragment file — FilterCells • Signac

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, ready for use with Signac functions.

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

Examples

fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
tmpf <- tempfile(fileext = ".gz")
FilterCells(
  fragments = fpath,
  cells = head(colnames(atac_small)),
  outfile = tmpf
)
#> 
#> Compressing filtered file
#> Indexing fragment file
file.remove(tmpf)
#> [1] TRUE