CreateAssay5Object

Create an <code>Assay5</code> object from a feature expression matrix;
the expected format of the matrix is features x cells

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

CreateAssay5Object function

<dl><dt>counts</dt>
<dd>A two-dimensional expression matrix</dd>
<dt>data</dt>
<dd>Optional prenormalized data matrix</dd>
<dt>min.cells</dt>
<dd>Include features detected in at least this many cells;
will subset the counts matrix as well. To reintroduce excluded features,
create a new object with a lower cutoff</dd>
<dt>min.features</dt>
<dd>Include cells where at least this many features
are detected</dd>
<dt>csum</dt>
<dd>Function for calculating cell sums</dd>
<dt>fsum</dt>
<dd>Function for calculating feature sums</dd>
<dt>...</dt>
<dd>Arguments passed to other methods</dd></dl>

Arguments

Create a v5 Assay object — CreateAssay5Object

<dl>

<dt>counts</dt>
<dd>A two-dimensional expression matrix</dd>


<dt>data</dt>
<dd>Optional prenormalized data matrix</dd>


<dt>min.cells</dt>
<dd>Include features detected in at least this many cells;
will subset the counts matrix as well. To reintroduce excluded features,
create a new object with a lower cutoff</dd>


<dt>min.features</dt>
<dd>Include cells where at least this many features
are detected</dd>


<dt>csum</dt>
<dd>Function for calculating cell sums</dd>


<dt>fsum</dt>
<dd>Function for calculating feature sums</dd>


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

</dl>

Create a v5 Assay object

CreateAssay5Object: Create a v5 Assay object

Description

Usage

Value

Arguments