CountFragments function

Count fragments

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. If a list of fragment files is provided, the total fragments for each cell barcode across all files will be returned
• 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

Returns

Returns a data.frame with the following columns:

• CB: the cell barcode
• frequency_count: total number of fragments sequenced for the cell
• mononucleosome: total number of fragments with length between 147 bp and 294 bp
• nucleosome_free: total number of fragments with length <147 bp
• reads_count: total number of reads sequenced for the cell

Examples

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