Extract Expression Matrix from Seurat, SummarizedExperiment, or Matrix

Extracts a gene expression matrix from a Seurat object (default assay and "data" slot), a SummarizedExperiment object (assay named "logcounts"), or returns the input matrix if it is already a dense or sparse matrix.

Usage

extractData(data)

Arguments

data

A Seurat object, a SummarizedExperiment object, a dense numeric matrix, or a sparse matrix of class dgCMatrix

Value

A numeric gene expression matrix (dense or sparse), with genes as rows and cells or spots as columns.

Examples

seu_sc <- readRDS(system.file("extdata", "seu_sc.rds",
    package = "RankMap"
))

# From Seurat object:
mat <- extractData(seu_sc)