deconvolute_timer.default: Deconvolute Tumor Microenvironment Using TIMER

In IOBR/IOBR: Immune Oncology Biological Research

Deconvolute Tumor Microenvironment Using TIMER

Description

This function performs deconvolution of the tumor microenvironment using the TIMER algorithm. It processes multiple cancer datasets, removes batch effects, and estimates immune cell type abundances. The function relies on specific data and helper functions to manage the expression data and analyze the tumor microenvironment.

Usage

deconvolute_timer.default(args)

Arguments

args	An environment or list containing parameters and file paths necessary for the function to execute. This should include 'outdir' for output directory, 'batch' for a file containing paths to expression data and cancer types.

Value

Returns a matrix of abundance scores for different immune cell types across multiple cancer samples.

Examples

args <- list(
  outdir = "path/to/output",
  batch = "path/to/batch.csv"
)
results <- deconvolute_timer.default(args)

IOBR/IOBR documentation built on April 3, 2025, 2:19 p.m.