FilterFragments

Remove cells from a fragments file that are not present in a given list of cells. Note that this reads the whole fragments file into memory, so may require a lot of memory depending on the size of the fragments file.

FilterFragments(
  fragment.path,
  cells,
  output.path,
  assume.sorted = FALSE,
  compress = TRUE,
  index = TRUE,
  verbose = TRUE,
  ...
)

Arguments

fragment.path	Path to a tabix-indexed fragments file
cells	A vector of cells to retain
output.path	Name and path for output tabix file. A tabix index file will also be created in the same location, with the .tbi file extension.
assume.sorted	Assume sorted input and don't sort the filtered file. Can save a lot of time, but indexing will fail if assumption is wrong.
compress	Compress filtered fragments using bgzip (default TRUE)
index	Index the filtered tabix file (default TRUE)
verbose	Display messages
...	Additional arguments passed to fread

Value

None

Examples

# \donttest{
fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
output.path = file.path(tempdir(), "filtered.tsv")

FilterFragments(
  fragment.path = fpath,
  cells = colnames(atac_small),
  output.path = output.path
)
#> Retaining 100 cells
#> Reading fragments
#> Sorting fragments
#> Writing output
#> Compressing output
#> Building index
# }