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Correct for Batch Effects

batch_correct.Rd

This function uses the removeBatchEffect method from the limma package to adjust for known batch effects in the data.

Usage

batch_correct(object, batch_variable, bio_variables = NULL)

# S4 method for class 'SummarizedExperiment,character'
batch_correct(object, batch_variable, bio_variables = NULL)

Arguments

object

A SummarizedExperiment object. The first assay will be used.

batch_variable

A single character string specifying the column name in colData(object) that contains the batch information.

bio_variables

An optional character vector of column names in colData(object) that correspond to biological variables of interest. These effects will be preserved during the correction. If NULL (the default), only an intercept is protected.

Value

A SummarizedExperiment object with a new assay named "corrected" containing the batch-corrected data.

Functions

  • batch_correct(object = SummarizedExperiment, batch_variable = character): Method for SummarizedExperiment objects.

Examples

# --- Create a sample SummarizedExperiment object ---
set.seed(123)
counts <- matrix(rnorm(100 * 6, mean = 10, sd = 2), nrow = 100, ncol = 6)
colnames(counts) <- paste0("Sample", 1:6)

sample_info <- data.frame(
  row.names = colnames(counts),
  Condition = rep(c("A", "B"), each = 3),
  Batch = rep(c("Batch1", "Batch2"), times = 3)
)

se <- SummarizedExperiment(assays = list(log_intensities = counts),
                           colData = sample_info)
#> Error in SummarizedExperiment(assays = list(log_intensities = counts),     colData = sample_info): could not find function "SummarizedExperiment"

# --- Run batch correction, preserving the "Condition" variable ---
corrected_se <- batch_correct(se,
                              batch_variable = "Batch",
                              bio_variables = "Condition")
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'batch_correct': object 'se' not found

# --- Inspect the result ---
assayNames(corrected_se) # Now includes "corrected"
#> Error in assayNames(corrected_se): could not find function "assayNames"