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.

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

Assay-class function

<dl class="dl-horizontal">
<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>key</code></dt><dd>Key for the Assay</dd><dt><code>assay.orig</code></dt><dd>Original assay that this assay is based off of. Used to track
assay provenence</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>Utility slot for storing additional data associated with the assay</dd>

Slots

The Assay Class — Assay-class

The Assay Class

Assay-class: The Assay Class

Description

Arguments

Slots