CreateAssayObject: 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,
  key = NULL,
  check.matrix = FALSE,
  ...
)

Value

A Assay object

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
key: Optional key to initialize assay with
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.

Examples

Run this code

if (FALSE) {
pbmc_raw <- read.table(
  file = system.file('extdata', 'pbmc_raw.txt', package = 'Seurat'),
  as.is = TRUE
)
pbmc_rna <- CreateAssayObject(counts = pbmc_raw)
pbmc_rna
}

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