SeuratObject: CreateAssayObject – R documentation

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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.
`...`	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)

SeuratObject

Data Structures for Single Cell Data

v4.0.1

GPL-3

Authors

Rahul Satija [aut] (<https://orcid.org/0000-0001-9448-8833>), Andrew Butler [aut] (<https://orcid.org/0000-0003-3608-0463>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Tim Stuart [aut] (<https://orcid.org/0000-0002-3044-0897>), Jeff Farrell [ctb], Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Patrick Roelli [ctb], Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>)

Initial release

2021-05-07