normalize_batches: Normalize batches

In antonvsdata/notame: Workflow for non-targeted LC-MS metabolic profiling

Normalize batches

Description

Normalize bathces by either reference samples of population median. Uses normalizeBatches function from the batchCorr package

Usage

normalize_batches(object, batch, group, ref_label, population = "all", ...)

Arguments

object	a MetaboSet object
batch, group	character, column names of pData with batch labels and group labels
ref_label	the label of the reference group i.e. the group that is constant through batches
population	Identifier of population samples in group column (all (default) or any type of samples present in group)
...	additional parameters passed to batchCorr::normalizeBatches

Value

list, the object with normalized features and information on which features were corrected by ref samples in each batch.

Examples

# Batch correction
## Not run: 
batch_corrected <- normalize_batches(merged_sample, batch = "Batch", group = "QC", ref_label = "QC")
# Evaluate batch correction
pca_bhattacharyya_dist(merged_sample, batch = "Batch")
pca_bhattacharyya_dist(batch_corrected, batch = "Batch")

## End(Not run)

antonvsdata/notame documentation built on Sept. 14, 2024, 11:09 p.m.