pqn_norm: Probabilistic Quotient Normalisation (PQN)

In computational-metabolomics/structToolbox: Data processing & analysis tools for Metabolomics and other omics

Probabilistic Quotient Normalisation (PQN)

Description

PQN is used to normalise for differences in concentration between samples. It makes use of Quality Control (QC) samples as a reference. PQN scales by the median change relative to the reference in order to be more robust against changes caused by response to perturbation.

Usage

pqn_norm(
  qc_label = "QC",
  factor_name,
  qc_frac = 0,
  sample_frac = 0,
  ref_method = "mean",
  ref_mean = NULL,
  ...
)

Arguments

qc_label	(character) The label used to identify QC samples. The default is "QC".
factor_name	(character) The name of a sample-meta column to use.
qc_frac	(numeric) A value between 0 and 1 to indicate the minimum proportion of QC samples a feature must be present in for it to be included when computing the reference. Default qc_frac = 0. . The default is 0.
sample_frac	(numeric) A value between 0 and 1 to indicate the minimum proportion of samples a feature must be present in for it to be considered when computing the normalisation coefficients. . The default is 0.
ref_method	(character) Reference computation method. Allowed values are limited to the following: "mean": The reference is computed as the mean of the samples matching the qc_label input. "median": The reference is computed as the median of the samples matching the qc_label_input. The default is "mean".
ref_mean	(numeric, NULL) A single sample to use as the reference for normalisation. If set to NULL then the reference will be computed based on the other input parameters (ref_mean, qc_label etc). . The default is NULL.
...	Additional slots and values passed to struct_class.

Details

This object makes use of functionality from the following packages:

• pmp

Value

A pqn_norm object with the following output slots:

normalised	(DatasetExperiment) A DatasetExperiment object containing the normalised data.
coeff	(data.frame) The normalisation coefficients calculated by PQN.

Inheritance

A pqn_norm object inherits the following struct classes:

⁠[pqn_norm]⁠ >> ⁠[model]⁠ >> ⁠[struct_class]⁠

References

Jankevics A, Lloyd GR, Weber RJM (2023). pmp: Peak Matrix Processing and signal batch correction for metabolomics datasets. doi:10.18129/B9.bioc.pmp https://doi.org/10.18129/B9.bioc.pmp, R package version 1.14.0, https://bioconductor.org/packages/pmp.

Examples

M = pqn_norm(
      qc_label = "QC",
      factor_name = "V1",
      qc_frac = 0,
      sample_frac = 0,
      ref_mean = NULL,
      ref_method = "mean")

D = iris_DatasetExperiment()
M = pqn_norm(factor_name='Species',qc_label='all')
M = model_apply(M,D)

computational-metabolomics/structToolbox documentation built on Feb. 12, 2024, 2:15 a.m.