The Assay Class

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.

Slots

counts

Unnormalized data such as raw counts or TPMs

data

Normalized expression data

scale.data

Scaled expression data

assay.orig

Original assay that this assay is based off of. Used to track assay provenance

var.features

Vector of features exhibiting high variance across single cells

meta.features

Feature-level metadata

misc

A named list of unstructured miscellaneous data

key

A one-length character vector with the object's key; keys must be one or more alphanumeric characters followed by an underscore “_” (regex pattern “^[a-zA-Z][a-zA-Z0-9]*_$ ”)

See also

v3 Assay object, validity, and interaction methods: $.Assay(), Assay-validity, CreateAssayObject(), [.Assay(), [[.Assay(), dim.Assay(), dimnames.Assay(), merge.Assay(), split.Assay(), subset.Assay()