normalize_batches: Normalize batches

In antonvsdata/amp: Smoothing Metabolomics Analyses

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, ...)

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
...	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
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")

antonvsdata/amp documentation built on Jan. 8, 2020, 3:15 a.m.