Get and Set Assay Data

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, ...)

SetAssayData(object, layer, new.data, slot = deprecated(), ...)

# S3 method for Seurat
GetAssayData(object, assay = NULL, layer = NULL, slot = deprecated(), ...)

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

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

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

Arguments

object

An object

...

Arguments passed to other methods

layer

Name of layer to get or set

new.data

New assay data to add

slot

Specific assay data to get or set

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

Lifecycle

GetAssayData and SetAssayData have been superseded. To fetch expression matrices, use LayerData; to set expression data, use LayerData<-

Examples

# Get assay data from the default assay in a Seurat object
GetAssayData(object = pbmc_small, layer = "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 layer through the Seurat object
count.data <- GetAssayData(object = pbmc_small[["RNA"]], layer = "counts")
count.data <- as.matrix(x = count.data + 1)
new.seurat.object <- SetAssayData(
    object = pbmc_small,
    layer = "counts",
    new.data = count.data,
    assay = "RNA"
)

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