Deconvolute Tumor Microenvironment Using TIMER

Performs deconvolution of the tumor microenvironment using the TIMER algorithm. Processes multiple cancer datasets, removes batch effects, and estimates immune cell type abundances.

Usage

deconvolute_timer.default(args)

Arguments

args

List or environment containing parameters:

outdir

Character. Output directory path.

batch

Character. File containing paths to expression data and cancer types.

Value

Matrix of abundance scores for different immune cell types across multiple cancer samples.

Examples

if (FALSE) { # \dontrun{
set.seed(123)
immune <- load_data("immuneCuratedData")
cancer_genes <- load_data("cancer_type_genes")
if (!is.null(immune) && !is.null(cancer_genes)) {
  gene_names <- unique(c(head(rownames(immune$genes), 30), cancer_genes[["stad"]]))
  sample_names <- paste0("Sample", 1:2)
  n_genes <- length(gene_names)
  expr <- matrix(runif(n_genes * 2, 1, 100), n_genes, 2,
                 dimnames = list(gene_names, sample_names))
  tf <- tempfile(fileext = ".tsv")
  write.table(as.data.frame(expr), tf, sep = "\t", quote = FALSE)
  batch_tf <- tempfile(fileext = ".csv")
  write.table(data.frame(path = tf, type = "stad"), batch_tf,
              sep = ",", col.names = FALSE, row.names = FALSE, quote = FALSE)
  args <- list(outdir = tempdir(), batch = batch_tf)
  result <- deconvolute_timer.default(args)
  if (!is.null(result)) head(result)
}
} # }