Default Assay

Get and set the default assay

DefaultAssay(object, ...)

DefaultAssay(object, ...) <- value

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

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

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

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

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

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

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

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

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

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

# S3 method for 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)
#> [1] "RNA"

# 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)
#> [1] "RNA2"