IntersectMatrix

Remove or retain matrix rows that intersect given genomic regions

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

IntersectMatrix function

<dl><dt>matrix</dt>
<dd>A matrix with genomic regions in the rows</dd>
<dt>regions</dt>
<dd>A set of genomic regions to intersect with regions in the
matrix. Either a vector of strings encoding the genomic coordinates, or a
GRanges object.</dd>
<dt>invert</dt>
<dd>Discard rows intersecting the genomic regions supplied, rather
than retain.</dd>
<dt>sep</dt>
<dd>A length-2 character vector containing the separators to be used
for extracting genomic coordinates from a string. The first element will be
used to separate the chromosome name from coordinates, and the second element
used to separate start and end coordinates.</dd>
<dt>verbose</dt>
<dd>Display messages</dd>
<dt>...</dt>
<dd>Additional arguments passed to <code>findOverlaps</code></dd></dl>

Arguments

Intersect genomic coordinates with matrix rows — IntersectMatrix

<dl>

<dt>matrix</dt>
<dd>A matrix with genomic regions in the rows</dd>


<dt>regions</dt>
<dd>A set of genomic regions to intersect with regions in the
matrix. Either a vector of strings encoding the genomic coordinates, or a
GRanges object.</dd>


<dt>invert</dt>
<dd>Discard rows intersecting the genomic regions supplied, rather
than retain.</dd>


<dt>sep</dt>
<dd>A length-2 character vector containing the separators to be used
for extracting genomic coordinates from a string. The first element will be
used to separate the chromosome name from coordinates, and the second element
used to separate start and end coordinates.</dd>


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


<dt>...</dt>
<dd>Additional arguments passed to <code>findOverlaps</code></dd>

</dl>

IntersectMatrix: Intersect genomic coordinates with matrix rows

Description

Usage

Value

Arguments

Examples