DimReduc-validity

Validation of <code>DimReduc</code> objects is handled by
<code><a href="/link/validObject?package=SeuratObject&version=5.0.2" data-mini-rdoc="SeuratObject::validObject">validObject</a></code>

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

DimReduc-validity function

The cell embeddings matrix must be a numeric matrix of dimensions
\(n_{cells}\) by \(d_{dimensions}\); row names must be the cell names
and column names must be the dimension identifier. The dimension identifier
must be &#8220;<code>key_dimension</code>&#8221; (eg. &#8220;<code>PC_1</code>&#8221;). Dimension
identifiers must be in order and cannot be skipped

Cell Embeddings Validation

Feature and Projected Feature Loadings Validation

Standard Deviations Validation

Keys must be a one-length character vector; a key must be composed of one
of the following:<ul>
<li>An empty string (eg. &#8220;<code>''</code>&#8221;) where <code>nchar() == 0</code></li>
<li>An string composed of one or more alphanumeric values
 (both lower- and upper-case) that ends with an underscore
 (&#8220;<code>_</code>&#8221;); the first character must be a letter</li>
</ul>Keys that are not empty strings are validated with the regex
&#8220;<code>SeuratObject:::.KeyPattern()</code>&#8221;

Key Validation

Validation of <code>DimReduc</code> objects is handled by
<code><a href='https://rdrr.io/r/methods/validObject.html'>validObject</a></code>

Dimensional Reduction Validity — DimReduc-validity

The cell embeddings matrix must be a numeric matrix of dimensions
\(n_{cells}\) by \(d_{dimensions}\); row names must be the cell names
and column names must be the dimension identifier. The dimension identifier
must be &#8220;<code>key_dimension</code>&#8221; (eg. &#8220;<code>PC_1</code>&#8221;). Dimension
identifiers must be in order and cannot be skipped

Keys must be a one-length character vector; a key must be composed of one
of the following:<ul>
<li>An empty string (eg. &#8220;<code>''</code>&#8221;) where <code>nchar() == 0</code></li>
<li>An string composed of one or more alphanumeric values
 (both lower- and upper-case) that ends with an underscore
 (&#8220;<code>_</code>&#8221;); the first character must be a letter</li>
</ul>Keys that are not empty strings are validated with the regex
&#8220;<code>SeuratObject:::.KeyPattern()</code>&#8221;

DimReduc-validity: Dimensional Reduction Validity

Description

Arguments

Cell Embeddings Validation

Feature and Projected Feature Loadings Validation

Standard Deviations Validation

Key Validation

See Also