Layers-StdAssay

LayerData.StdAssay

LayerData&lt;-.StdAssay

Layers.StdAssay

internal

Defines S4 classes for single-cell genomic data and associated
information, such as dimensionality reduction embeddings, nearest-neighbor
graphs, and spatially-resolved coordinates. Provides data access methods and
R-native hooks to ensure the Seurat object is familiar to other R users. See
Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>,
Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>,
and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>,
Hao Y, Hao S, et al (2021) <doi:10.1016/j.cell.2021.04.048> and
Hao Y, et al (2023) <doi:10.1101/2022.02.24.481684> for
more details.

Paul Hoffman

SeuratObject

Data Structures for Single Cell Data

Rahul Satija

David Collins

Yuhan Hao

Austin Hartman

Gesmira Molla

Andrew Butler

Tim Stuart

Madeline Kowalski

Saket Choudhary

Skylar Li

Longda Jiang

Jeff Farrell

Shiwei Zheng

Christoph Hafemeister

Patrick Roelli

Layers-StdAssay function

<dl><dt>object</dt>
<dd>An object</dd>
<dt>layer</dt>
<dd>Name of layer to fetch or set</dd>
<dt>features, cells</dt>
<dd>Vectors of features/cells to include</dd>
<dt>fast</dt>
<dd>Determine how to return the layer data; choose from:<dl>
 <dt><code>FALSE</code></dt>
<dd>Apply any transpositions and attempt to add
 feature/cell names (if supported) back to the layer data</dd></dl></dd> <dt><code>NA</code></dt>
<dd>Attempt to add feature/cell names back to the layer data,
 skip any transpositions</dd> <dt><code>TRUE</code></dt>
<dd>Do not apply any transpositions or add feature/cell
 names to the layer data</dd>
</dl>
<dt>slot</dt>
<dd>lifecycle::badge("deprecated")</dd>
<dt>...</dt>
<dd>Arguments passed to other methods</dd>
<dt>value</dt>
<dd>New two-dimensional data to be added as a layer</dd>
<dt>search</dt>
<dd>A pattern to search layer names for; pass one of:<ul>
<li>&#8220;<code>NA</code>&#8221; to pull all layers</li>
<li>&#8220;<code>NULL</code>&#8221; to pull the default layer(s)</li>
<li>a <a href="/link/regular%20expression?package=SeuratObject&version=5.0.2" data-mini-rdoc="SeuratObject::regular expression">regular expression</a> that matches layer names</li>
</ul></dd>

Arguments

Query and Manipulate Assay Layers — Layers-StdAssay

<dl>

<dt>object</dt>
<dd>An object</dd>


<dt>layer</dt>
<dd>Name of layer to fetch or set</dd>


<dt>features, cells</dt>
<dd>Vectors of features/cells to include</dd>


<dt>fast</dt>
<dd>Determine how to return the layer data; choose from:<dl>
 <dt><code>FALSE</code></dt>
<dd>Apply any transpositions and attempt to add
 feature/cell names (if supported) back to the layer data</dd>

 <dt><code>NA</code></dt>
<dd>Attempt to add feature/cell names back to the layer data,
 skip any transpositions</dd>

 <dt><code>TRUE</code></dt>
<dd>Do not apply any transpositions or add feature/cell
 names to the layer data</dd>


</dl></dd>


<dt>slot</dt>
<dd>lifecycle::badge("deprecated")</dd>


<dt>...</dt>
<dd>Arguments passed to other methods</dd>


<dt>value</dt>
<dd>New two-dimensional data to be added as a layer</dd>


<dt>search</dt>
<dd>A pattern to search layer names for; pass one of:<ul>
<li>&#8220;<code>NA</code>&#8221; to pull all layers</li>
<li>&#8220;<code>NULL</code>&#8221; to pull the default layer(s)</li>
<li>a <a href='https://rdrr.io/r/base/grep.html'>regular expression</a> that matches layer names</li>
</ul></dd>

</dl>

Query and Manipulate Assay Layers

Layers-StdAssay: Query and Manipulate Assay Layers

Description

Usage

Value

Arguments