Fragment-class

Fragment

The Fragment class is designed to hold information needed for working with
fragment files.

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

Fragment-class function

<dl>
<dt><code>path</code></dt>
<dd>Path to the fragment file on disk.
See <a href="https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/output/fragments">https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/output/fragments</a></dd></dl>
<dt><code>hash</code></dt>
<dd>A vector of two md5sums: first element is the md5sum of the
fragment file, the second element is the md5sum of the index.</dd>
<dt><code>cells</code></dt>
<dd>A named vector of cells where each element is the cell barcode
as it appears in the fragment file, and the name of each element is the
corresponding cell barcode as stored in the ChromatinAssay object.</dd>

Slots

The Fragment class — Fragment-class

<dl>
<dt><code>path</code></dt>
<dd>Path to the fragment file on disk.
See <a href='https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/output/fragments'>https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/output/fragments</a></dd>


<dt><code>hash</code></dt>
<dd>A vector of two md5sums: first element is the md5sum of the
fragment file, the second element is the md5sum of the index.</dd>


<dt><code>cells</code></dt>
<dd>A named vector of cells where each element is the cell barcode
as it appears in the fragment file, and the name of each element is the
corresponding cell barcode as stored in the ChromatinAssay object.</dd>


</dl>

Fragment-class: The Fragment class

Description

Arguments

Slots