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Extract cell counts

Source: R/cellCounts.R
cellCounts.Rd

Extract matrix of cell counts from SingleCellExperiment

Usage

cellCounts(x)

Arguments

x

a SingleCellExperiment

Value

matrix of cell counts with samples as rows and cell types as columns

See also

computeCellCounts()

Examples

library(muscat)
library(SingleCellExperiment)

data(example_sce)

# create pseudobulk for each sample and cell cluster
pb <- aggregateToPseudoBulk(example_sce,
  assay = "counts",
  cluster_id = "cluster_id",
  sample_id = "sample_id",
  verbose = FALSE
)

# get matrix of cell counts for each sample
cellCounts(pb)
#>         B cells CD14+ Monocytes CD4 T cells CD8 T cells FCGR3A+ Monocytes
#> ctrl101     100             100         100          74                80
#> ctrl107      44             100         100          20                32
#> stim101     100             100         100         100               100
#> stim107      54             100         100          15                37