Assay

The Assay class is where expression data is stored.

Slots

Slot	Function
counts	Stores unnormalized data such as raw counts or TPMs
data	Normalized data matrix
scale.data	Scaled data matrix
key	...
var.features	A vector of features identified as variable
meta.features	Feature-level meta data

Data Access

Accessing data from an Assay object is done in several ways. Expression data is accessed with the GetAssayData function. Pulling expression data from the data slot can also be done with the single [ extract operator. Adding expression data to either the counts, data, or scale.data slots can be done with SetAssayData. New data must have the same cells in the same order as the current expression data. Data added to counts or data must have the same features as the current expression data.

Feature-level meta data can be accessed with the double [[ extract operator. Adding feature-level meta data can be set using the double [[ extract operator as well. The HVFInfo function serves a specific version of the double [[ extract operator, pulling certain columns from the meta data.

The vector of variable features can be pulled with the VariableFeatures function. VariableFeatures can also set the vector of variable features.

The key ...

Methods

Methods for the Assay class can be found with the following:

library(Seurat)
utils::methods(class = 'Assay')