R: Get and Set Assay Data

AssayData {SeuratObject} | R Documentation

## Get and Set Assay Data

### Description

General accessor and setter functions for `Assay` objects. `GetAssayData` can be used to pull information from any of the expression matrices (eg. “counts”, “data”, or “scale.data”). `SetAssayData` can be used to replace one of these expression matrices

### Usage

    GetAssayData(object, slot, ...)

    SetAssayData(object, slot, new.data, ...)

    ## S3 method for class 'Seurat'
    GetAssayData(object, slot = "data", assay = NULL, ...)

    ## S3 method for class 'Seurat'
    SetAssayData(object, slot = "data", new.data, assay = NULL, ...)

    ## S3 method for class 'Assay'
    GetAssayData(object, slot = c("data", "scale.data", "counts"), ...)

    ## S3 method for class 'Assay'
    SetAssayData(object, slot = c("data", "scale.data", "counts"), new.data, ...)

### Arguments

`object` | An object
`slot` | Specific assay data to get or set
`...` | Arguments passed to other methods
`new.data` | New assay data to add
`assay` | Specific assay to get data from or set data for; defaults to the default assay

### Value

`GetAssayData`: returns the specified assay data

`SetAssayData`: `object` with the assay data set

### Examples

    # Get assay data from the default assay in a Seurat object
    GetAssayData(object = pbmc_small, slot = "data")[1:5,1:5]

    # Set an Assay slot through the Seurat object
    count.data <- GetAssayData(object = pbmc_small[["RNA"]], slot = "counts")
    count.data <- as.matrix(x = count.data + 1)
    new.seurat.object <- SetAssayData(
        object = pbmc_small,
        slot = "counts",
        new.data = count.data,
        assay = "RNA"
    )

    # Get the data directly from an Assay object
    GetAssayData(pbmc_small[["RNA"]], slot = "data")[1:5,1:5]

    # Set an Assay slot directly
    count.data <- GetAssayData(pbmc_small[["RNA"]], slot = "counts")
    count.data <- as.matrix(x = count.data + 1)
    new.assay <- SetAssayData(pbmc_small[["RNA"]], slot = "counts", new.data = count.data)

[Package SeuratObject version 4.0.3 Index]