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, ...)
SetAssayData(object, layer, new.data, slot = deprecated(), ...)
## S3 method for class 'Seurat'
GetAssayData(object, assay = NULL, layer = NULL, slot = deprecated(), ...)
## S3 method for class 'Seurat'
SetAssayData(
object,
layer = "data",
new.data,
slot = deprecated(),
assay = NULL,
...
)
## S3 method for class 'Assay'
GetAssayData(
object,
layer = c("data", "scale.data", "counts"),
slot = deprecated(),
...
)
## S3 method for class '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 |
|
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have been superseded.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]
# 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]
# 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)
[Package SeuratObject version 5.0.2 Index]