DefaultAssay: Default Assay

In SeuratObject: Data Structures for Single Cell Data

Default Assay

Description

Get and set the default assay

Usage

DefaultAssay(object, ...)

DefaultAssay(object, ...) <- value

## S3 method for class 'Graph'
DefaultAssay(object, ...)

## S3 replacement method for class 'Graph'
DefaultAssay(object, ...) <- value

## S3 method for class 'Assay'
DefaultAssay(object, ...)

## S3 replacement method for class 'Assay'
DefaultAssay(object, ...) <- value

## S3 method for class 'Assay5'
DefaultAssay(object, ...)

## S3 replacement method for class 'Assay5'
DefaultAssay(object, ...) <- value

## S3 method for class 'SeuratCommand'
DefaultAssay(object, ...)

## S3 method for class 'DimReduc'
DefaultAssay(object, ...)

## S3 replacement method for class 'DimReduc'
DefaultAssay(object, ...) <- value

## S3 method for class 'Seurat'
DefaultAssay(object, ...)

## S3 replacement method for class 'Seurat'
DefaultAssay(object, ...) <- value

Arguments

object	An object
...	Arguments passed to other methods
value	Name of assay to set as default

Value

DefaultAssay: The name of the default assay

DefaultAssay<-: An object with the default assay updated

Examples

# Get current default assay
DefaultAssay(object = pbmc_small)

# Create dummy new assay to demo switching default assays
new.assay <- pbmc_small[["RNA"]]
Key(object = new.assay) <- "RNA2_"
pbmc_small[["RNA2"]] <- new.assay
# switch default assay to RNA2
DefaultAssay(object = pbmc_small) <- "RNA2"
DefaultAssay(object = pbmc_small)

SeuratObject documentation built on Nov. 18, 2023, 1:06 a.m.