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.

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> for
more details.

Paul Hoffman

SeuratObject

Data Structures for Single Cell Data

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 provenance</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

See Also