CountFragments: Count fragments

In wzthu/ATACpipe: An Easy-to-use Systematic pipeline for ATACseq data analysis

Count fragments

Description

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

Usage

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

Value

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="scUtils")
counts <- CountFragments(fragments = fpath)

wzthu/ATACpipe documentation built on Aug. 12, 2022, 7:38 a.m.