R: Default Assay

DefaultAssay {SeuratObject} | R Documentation

## 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 '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)

[Package SeuratObject version 4.1.0 Index]