CountFragments

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

A framework for the analysis and exploration of single-cell chromatin data.
The 'Signac' package contains functions for quantifying single-cell chromatin data,
computing per-cell quality control metrics, dimension reduction
and normalization, visualization, and DNA sequence motif analysis.
Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.

Tim Stuart

Signac

Analysis of Single-Cell Chromatin Data

Avi Srivastava

Paul Hoffman

Rahul Satija

CountFragments function

<dl><dt>fragments</dt>
<dd>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</dd>
<dt>cells</dt>
<dd>Cells to include. If NULL, include all cells</dd>
<dt>max_lines</dt>
<dd>Maximum number of lines to read from the fragment file. If
NULL, read all lines in the file.</dd>
<dt>verbose</dt>
<dd>Display messages</dd></dl>

Arguments

Count fragments — CountFragments

<dl>

<dt>fragments</dt>
<dd>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</dd>


<dt>cells</dt>
<dd>Cells to include. If NULL, include all cells</dd>


<dt>max_lines</dt>
<dd>Maximum number of lines to read from the fragment file. If
NULL, read all lines in the file.</dd>


<dt>verbose</dt>
<dd>Display messages</dd>

</dl>

CountFragments: Count fragments

Description

Usage

Value

Arguments

Examples