Count total fragments per cell barcode present in a fragment file.
CountFragments(fragments, cells = NULL, max_lines = NULL, verbose = TRUE)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 to include. If NULL, include all cells
Maximum number of lines to read from the fragment file. If NULL, read all lines in the file.
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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
fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
counts <- CountFragments(fragments = fpath)