RemoveBatchEffect: Remove Batch Effect of Expression Set

In IOBR: Immune Oncology Biological Research

Remove Batch Effect of Expression Set

Description

Removes batch effects between two gene expression datasets, typically representing different sample types such as cancer cells and immune cells. Uses ComBat from the sva package for batch correction.

Usage

RemoveBatchEffect(cancer.exp, immune.exp, immune.cellType)

Arguments

cancer.exp	Matrix or data frame. Cancer cell expression data with genes as rows and samples as columns.
immune.exp	Matrix or data frame. Immune cell expression data with genes as rows and samples as columns.
immune.cellType	Vector. Cell type for each column in 'immune.exp'.

Value

A list containing:

1

Batch effect corrected cancer expression data

2

Batch effect corrected immune expression data

3

Aggregated immune expression data (median per cell type)

Author(s)

Bo Li

Examples

set.seed(123)
gene_names <- paste0("Gene", 1:100)
sample_names_cancer <- paste0("CancerSample", 1:10)
cancer.exp <- matrix(runif(1000, 1, 1000),
  nrow = 100, ncol = 10,
  dimnames = list(gene_names, sample_names_cancer)
)

sample_names_immune <- paste0("ImmuneSample", 1:5)
immune.exp <- matrix(runif(500, 1, 1000),
  nrow = 100, ncol = 5,
  dimnames = list(gene_names, sample_names_immune)
)

immune.cellType <- c("T-cell", "B-cell", "T-cell", "NK-cell", "B-cell")
names(immune.cellType) <- sample_names_immune

result <- RemoveBatchEffect(cancer.exp, immune.exp, immune.cellType)
if (!is.null(result)) str(result)

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