DimReduc-class

DimReduc

The DimReduc object stores a dimensionality reduction taken out in Seurat; each DimReduc
consists of a cell embeddings matrix, a feature loadings matrix, and a projected feature
loadings matrix.

A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. 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 Butler A and Satija R (2017) <doi:10.1101/164889> for more details. Please note: SDMTools is available is available from the CRAN archives with install.packages("https://cran.rstudio.com//src/contrib/Archive/SDMTools/SDMTools_1.1-221.2.tar.gz", repos = NULL); it is not in the standard repositories.

Paul Hoffman

Seurat

Tools for Single Cell Genomics

Rahul Satija

Andrew Butler

Tim Stuart

Jeff Farrell

Shiwei Zheng

Christoph Hafemeister

Patrick Roelli

Yuhan Hao

DimReduc-class function

<dl class="dl-horizontal">
<dt><code>cell.embeddings</code></dt><dd>Cell embeddings matrix (required)</dd></dl><dt><code>feature.loadings</code></dt><dd>Feature loadings matrix (optional)</dd><dt><code>feature.loadings.projected</code></dt><dd>Projected feature loadings matrix (optional)</dd><dt><code>assay.used</code></dt><dd>Name of assay used to generate <code>DimReduc</code> object</dd><dt><code>global</code></dt><dd>Is this <code>DimReduc</code> global/persistent? If so, it will not be
removed when removing its associated assay</dd><dt><code>stdev</code></dt><dd>A vector of standard deviations</dd><dt><code>key</code></dt><dd>Key for the <code>DimReduc</code>, must be alphanumerics followed by an underscore</dd><dt><code>jackstraw</code></dt><dd>A <code><a rd-options="" href="/link/JackStrawData-class?package=Seurat&version=3.1.4" data-mini-rdoc="Seurat::JackStrawData-class">JackStrawData-class</a></code> object associated with
this <code>DimReduc</code></dd><dt><code>misc</code></dt><dd>Utility slot for storing additional data associated with the
<code>DimReduc</code> (e.g. the total variance of the PCA)</dd>

Slots

The Dimmensional Reduction Class — DimReduc-class

The Dimmensional Reduction Class

DimReduc-class: The Dimmensional Reduction Class

Description

Arguments

Slots