pca_bhattacharyya_dist: Bhattacharyya distance between bathces in PCA space

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

Bhattacharyya distance between bathces in PCA space

Description

Computes Bhattacharyya distance between all pairs of batches after projecting the samples into PCA space with pcaMethods::pca

Usage

pca_bhattacharyya_dist(
  object,
  batch,
  all_features = FALSE,
  center = TRUE,
  scale = "uv",
  nPcs = 3,
  ...
)

Arguments

object	a MetaboSet object
batch	column name of pData givinh the batch labels
all_features	logical, should all features be used? If FALSE (the default), flagged features are removed before imputation.
center	logical, should the data be centered prior to PCA? (usually yes)
scale	scaling used, as in pcaMethods::prep. Default is "uv" for unit variance
nPcs	the number of principal components to use
...	other parameters to pcaMethods::pca

Value

matrix of Bhattacharyya distances between batches

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.