Save the expression matrix of a simulated pseudo-bulk dataset to a file

Usage

save_simulation(simulation, filename, assay = "bulk_counts")

Arguments

simulation: the result of simulate_bulk()
filename: the filename where to save the expression matrix to
assay: name of the assay in simulation to save, default to bulk_counts

Value

write a file

Examples

counts <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol=300), sparse = TRUE)
tpm <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol=300), sparse = TRUE)
tpm <- Matrix::t(1e6*Matrix::t(tpm)/Matrix::colSums(tpm))

colnames(counts) <- paste0("cell_",rep(1:300))
colnames(tpm) <- paste0("cell_",rep(1:300))
rownames(counts) <- paste0("gene_",rep(1:1000))
rownames(tpm) <- paste0("gene_",rep(1:1000))

annotation <- data.frame("ID"=paste0("cell_",rep(1:300)),
                         "cell_type"=c(rep("T cells CD4",50),
                                       rep("T cells CD8",50),
                                       rep("Macrophages",100),
                                       rep("NK cells",10),
                                       rep("B cells",70),
                                       rep("Monocytes",20)))

dataset <- SimBu::dataset(annotation = annotation,
                          count_matrix = counts,
                          tpm_matrix = tpm,
                          name = "test_dataset")
#> Filtering genes...
#> Created dataset.

s <- SimBu::simulate_bulk(dataset,
                          scenario="even",
                          scaling_factor="NONE",
                          nsamples=10,
                          ncells=100)
#> Finished simulation.
                          
 save_simulation(s, tempfile())