deconvo_timer: Deconvolve Using TIMER
In IOBR: Immune Oncology Biological Research

deconvo_timer

R Documentation

Deconvolve Using TIMER

Description

TIMER deconvolution for cancer-specific immune estimation.

Usage

deconvo_timer(eset, project = NULL, indications = NULL)

Arguments

`eset`	Gene expression matrix.
`project`	Optional project name. Default is 'NULL'.
`indications`	Cancer type for each sample (e.g., '"brca"', '"stad"'). Must match number of columns in 'eset'.

Value

Data frame with TIMER cell fractions. Columns suffixed with '_TIMER'.

Author(s)

Dongqiang Zeng

Examples

## Not run: 
immune <- load_data("immuneCuratedData")
cancer_genes <- load_data("cancer_type_genes")
if (!is.null(immune) && !is.null(cancer_genes)) {
  set.seed(123)
  genes <- unique(c(head(rownames(immune$genes), 100), cancer_genes[["stad"]]))
  sim_eset <- matrix(rnorm(length(genes) * 2), length(genes), 2)
  rownames(sim_eset) <- genes
  colnames(sim_eset) <- paste0("Sample", 1:2)
  result <- deconvo_timer(eset = sim_eset, project = "TCGA-STAD",
                          indications = rep("stad", 2))
  if (!is.null(result)) head(result)
}

## End(Not run)

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