R: Create an Assay object

CreateAssayObject {SeuratObject} | R Documentation

## Create an Assay object

### Description

Create an Assay object from a feature (e.g. gene) expression matrix. The expected format of the input matrix is features x cells.

### Usage

    CreateAssayObject(
      counts,
      data,
      min.cells = 0,
      min.features = 0,
      check.matrix = FALSE,
      ...
    )

### Arguments

`counts` | Unnormalized data such as raw counts or TPMs
`data` | Prenormalized data; if provided, do not pass `counts`
`min.cells` | Include features detected in at least this many cells. Will subset the counts matrix as well. To reintroduce excluded features, create a new object with a lower cutoff.
`min.features` | Include cells where at least this many features are detected.
`check.matrix` | Check counts matrix for NA, NaN, Inf, and non-integer values
`...` | Arguments passed to `as.sparse`

### Details

Non-unique cell or feature names are not allowed. Please make unique before calling this function.

### Value

A `Assay` object

### Examples

    ## Not run:
    pbmc_raw <- read.table(
      file = system.file('extdata', 'pbmc_raw.txt', package = 'Seurat'),
      as.is = TRUE
    )
    pbmc_rna <- CreateAssayObject(counts = pbmc_raw)
    pbmc_rna

    ## End(Not run)

[Package SeuratObject version 4.1.0 Index]