Add gene counts to a SingleCellExperiment object

Add gene counts to a SingleCellExperiment object as an altExps slot named gene.

Usage

add_gene_counts(sce, gene_count_file)

Arguments

sce

A SingleCellExperiment object.

gene_count_file

The file path to the gene count file. If missing, the function will try to find the gene count file in the output directory.

Examples

# Set up a mock SingleCellExperiment object
sce <- SingleCellExperiment::SingleCellExperiment(
  assays = list(counts = matrix(0, nrow = 10, ncol = 10))
)
colnames(sce) <- paste0('cell', 1:10)
# Set up a mock gene count file
gene_count_file <- tempfile()
gene_mtx <- matrix(1:10, nrow = 2, ncol = 5)
colnames(gene_mtx) <- paste0('cell', 1:5)
rownames(gene_mtx) <- c("gene1", "gene2")
write.csv(gene_mtx, gene_count_file)
# Add gene counts to the SingleCellExperiment object
sce <- add_gene_counts(sce, gene_count_file)
# verify the gene counts are added
SingleCellExperiment::altExps(sce)$gene
#> class: SingleCellExperiment 
#> dim: 2 10 
#> metadata(0):
#> assays(1): counts
#> rownames(2): gene1 gene2
#> rowData names(0):
#> colnames(10): cell1 cell2 ... cell9 cell10
#> colData names(0):
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):