ruvs_qc: Remove Unwanted Variation

In antonvsdata/amp: Smoothing Metabolomics Analyses

Description

An interface for the RUVs method in RUVSeq package.

Usage

ruvs_qc(object, batch, replicates, k = 3, ...)

Arguments

object	a MetaboSet object
batch	the column name for batch labels
replicates	list of numeric vectors, indexes of replicates
k	The number of factors of unwanted variation to be estimated from the data.
...	other parameters passed to RUVSeq::RUVs

Value

a MetaboSet object with the normalized data

Examples

# Batch correction
replicates <- list(which(merged_sample$QC == "QC"))
batch_corrected <- ruvs_qc(merged_sample, batch = "Batch", replicates = replicates)
# 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.