pqn_normalization: Probabilistic quotient normalization

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

Probabilistic quotient normalization

Description

Apply probabilistic quotient normalization (PQN) to the exprs part of a MetaboSet object. By default, reference is calculated from high-quality QC samples and the median of the reference is used for normalization. Check parameters for more options.

Usage

pqn_normalization(
  object,
  ref = c("qc", "all"),
  method = c("median", "mean"),
  all_features = FALSE
)

Arguments

object	a MetaboSet object
ref	character, the type of reference samples to use for normalization.
method	character, the method to use for calculating the reference sample.
all_features	logical, should all features be used for calculating the reference sample?

Value

a MetaboSet object with altered feature abundances

Examples

pqn_set <- pqn_normalization(merged_sample)

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