deconvolute_timer.default: Deconvolute Tumor Microenvironment Using TIMER

In IOBR: Immune Oncology Biological Research

Deconvolute Tumor Microenvironment Using TIMER

Description

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

## Not run: 
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)
}

## End(Not run)

IOBR documentation built on May 30, 2026, 5:07 p.m.