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

GetAssayData(object, slot, ...)

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

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

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

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

# S3 method for 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]
#> 5 x 5 sparse Matrix of class "dgCMatrix"
#>         ATGCCAGAACGACT CATGGCCTGTGCAT GAACCTGATGAACC TGACTGGATTCTCA
#> MS4A1         .              .                     .              .
#> CD79B         4.968821       .                     .              .
#> CD79A         .              .                     .              .
#> HLA-DRA       .              4.776153              .              .
#> TCL1A         .              .                     .              .
#>         AGTCAGACTGCACA
#> MS4A1         .       
#> CD79B         .       
#> CD79A         .       
#> HLA-DRA       4.074201
#> TCL1A         .       

# 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]
#> 5 x 5 sparse Matrix of class "dgCMatrix"
#>         ATGCCAGAACGACT CATGGCCTGTGCAT GAACCTGATGAACC TGACTGGATTCTCA
#> MS4A1         .              .                     .              .
#> CD79B         4.968821       .                     .              .
#> CD79A         .              .                     .              .
#> HLA-DRA       .              4.776153              .              .
#> TCL1A         .              .                     .              .
#>         AGTCAGACTGCACA
#> MS4A1         .       
#> CD79B         .       
#> CD79A         .       
#> HLA-DRA       4.074201
#> TCL1A         .       

# 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)