Assay-class

Assay

The Assay object is the basic unit of Seurat; each Assay stores raw,
normalized, and scaled data as well as cluster information, variable
features, and any other assay-specific metadata. Assays should contain single
cell expression data such as RNA-seq, protein, or imputed expression data.

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

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

Assay-class function

<dl>
<dt><code>counts</code></dt>
<dd>Unnormalized data such as raw counts or TPMs</dd></dl>
<dt><code>data</code></dt>
<dd>Normalized expression data</dd>
<dt><code>scale.data</code></dt>
<dd>Scaled expression data</dd>
<dt><code>assay.orig</code></dt>
<dd>Original assay that this assay is based off of. Used to
track assay provenance</dd>
<dt><code>var.features</code></dt>
<dd>Vector of features exhibiting high variance across
single cells</dd>
<dt><code>meta.features</code></dt>
<dd>Feature-level metadata</dd>
<dt><code>misc</code></dt>
<dd>A named list of unstructured miscellaneous data</dd>
<dt><code>key</code></dt>
<dd>A one-length character vector with the object's key; keys must
be one or more alphanumeric characters followed by an underscore
&#8220;<code>_</code>&#8221; (regex pattern
&#8220;<code>SeuratObject:::.KeyPattern()</code>&#8221;)</dd>

Slots

The Assay Class — Assay-class

<dl>
<dt><code>counts</code></dt>
<dd>Unnormalized data such as raw counts or TPMs</dd>


<dt><code>data</code></dt>
<dd>Normalized expression data</dd>


<dt><code>scale.data</code></dt>
<dd>Scaled expression data</dd>


<dt><code>assay.orig</code></dt>
<dd>Original assay that this assay is based off of. Used to
track assay provenance</dd>


<dt><code>var.features</code></dt>
<dd>Vector of features exhibiting high variance across
single cells</dd>


<dt><code>meta.features</code></dt>
<dd>Feature-level metadata</dd>


<dt><code>misc</code></dt>
<dd>A named list of unstructured miscellaneous data</dd>


<dt><code>key</code></dt>
<dd>A one-length character vector with the object's key; keys must
be one or more alphanumeric characters followed by an underscore
&#8220;<code>_</code>&#8221; (regex pattern
&#8220;<code>SeuratObject:::.KeyPattern()</code>&#8221;)</dd>


</dl>

The Assay Class

Assay-class: The Assay Class

Description

Arguments

Slots

See Also