Count total fragments per cell barcode present in a fragment file.

CountFragments(fragments, cells = NULL, max_lines = NULL, verbose = TRUE)

Arguments

fragments

Path to a fragment file

cells

Cells to include. If NULL, include all cells

max_lines

Maximum number of lines to read from the fragment file. If NULL, read all lines in the file.

verbose

Display messages

Value

Returns a data.frame

Examples

fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
counts <- CountFragments(fragments = fpath)