CastAssay-StdAssay

CastAssay.StdAssay

Cast layers in v5 assays to other classes

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

CastAssay-StdAssay function

<dl><dt>object</dt>
<dd>An object</dd>
<dt>to</dt>
<dd>Either a class name or a function that takes a layer and returns
the same layer as a new class</dd>
<dt>layers</dt>
<dd>A vector of layers to cast; defaults to all layers</dd>
<dt>verbose</dt>
<dd>Show progress updates</dd>
<dt>...</dt>
<dd>If <code>to</code> is a function, arguments passed to <code>to</code></dd></dl>

Arguments

Cast Assay Layers — CastAssay-StdAssay

<dl>

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


<dt>to</dt>
<dd>Either a class name or a function that takes a layer and returns
the same layer as a new class</dd>


<dt>layers</dt>
<dd>A vector of layers to cast; defaults to all layers</dd>


<dt>verbose</dt>
<dd>Show progress updates</dd>


<dt>...</dt>
<dd>If <code>to</code> is a function, arguments passed to <code>to</code></dd>

</dl>

Cast Assay Layers

CastAssay-StdAssay: Cast Assay Layers

Description

Usage

Value

Arguments