Get cell counts with metadata

Get cell counts with metadata for each sample

Usage

computeCellCounts(sce, annotation, sampleIDs)

Arguments

sce

SingleCellExperiment

annotation

string indicating column in colData(sce) storing cell type annotations

sampleIDs

string indicating column in colData(sce) storing sample identifers

Value

matrix storing cell counts

Examples

library(muscat)
library(SingleCellExperiment)

data(example_sce)

counts <- computeCellCounts(example_sce, "cluster_id", "sample_id")

counts[1:4, 1:4]
#>         B cells CD14+ Monocytes CD4 T cells CD8 T cells
#> ctrl101     100             100         100          74
#> ctrl107      44             100         100          20
#> stim101     100             100         100         100
#> stim107      54             100         100          15