Seurat (version 3.1.1)

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)

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.

Details

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

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

# }