Get expression data from Assay5 or Seurat object

A re-implementation of the SeuratObject::GetAssayData function to compatible with Assay5 objects.

Usage

GetAssayData5(object, ...)

# S3 method for class 'Seurat'
GetAssayData5(object, layer = "counts", assay = NULL, verbose = TRUE, ...)

# S3 method for class 'Assay5'
GetAssayData5(
  object,
  layer = "counts",
  join_layers = TRUE,
  verbose = TRUE,
  ...
)

# S3 method for class 'Assay'
GetAssayData5(object, layer = "counts", verbose = TRUE, ...)

Arguments

object

An object

...

Additional arguments passed to SeuratObject::GetAssayData.

layer

Name of layer to get or set

assay

Specific assay to get data from or set data for; defaults to the default assay

verbose

Whether to print the message. Default is TRUE.

join_layers

Whether to join layers if provided an `Assay5` object. Default is `TRUE`.

Value

A matrix or data frame containing the assay data.

See also

SeuratObject::GetAssayData

Examples

data(pancreas_sub)
GetAssayData5(
  pancreas_sub,
  layer = "counts",
  assay = "RNA"
)[1:5, 1:5]
#> 5 x 5 sparse Matrix of class "dgCMatrix"
#>               AAACCTGAGCCTTGAT AAACCTGGTAAGTGGC AAACGGGAGATATGGT
#> Xkr4                         .                .                .
#> Mrpl15                       .                .                .
#> Npbwr1                       .                .                .
#> 4732440D04Rik                .                .                .
#> Gm26901                      1                .                .
#>               AAACGGGCAAAGAATC AAACGGGGTACAGTTC
#> Xkr4                         .                .
#> Mrpl15                       .                .
#> Npbwr1                       .                .
#> 4732440D04Rik                .                .
#> Gm26901                      .                .

data(panc8_sub)
GetAssayData5(
  panc8_sub,
  layer = "counts",
  assay = "RNA"
)[1:5, 1:5]
#> 5 x 5 sparse Matrix of class "dgCMatrix"
#>         D101_13 D101_22 D101_43  D101_50   D102_7
#> A1CF   3.017717       .       . .        .       
#> A4GALT .              .       . .        .       
#> AAAS   .              .       . .        .       
#> AACS   .              .       . 1.001958 2.007853
#> AADAC  .              .       . .        .