Signac: FilterCells – R documentation

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FilterCells

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, ready for use with Signac functions.

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

Examples

fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
tmpf <- tempfile(fileext = ".gz")
FilterCells(
  fragments = fpath,
  cells = head(colnames(atac_small)),
  outfile = tmpf
)
file.remove(tmpf)

Signac

Analysis of Single-Cell Chromatin Data

v1.2.1

MIT + file LICENSE

Authors

Tim Stuart [aut, cre] (<https://orcid.org/0000-0002-3044-0897>), Avi Srivastava [aut] (<https://orcid.org/0000-0001-9798-2079>), Paul Hoffman [ctb] (<https://orcid.org/0000-0002-7693-8957>), Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>)

Initial release

2021-05-11