sb_corr: Signal/batch correction for mass spectrometry data

In structToolbox: Data processing & analysis tools for Metabolomics and other omics

Description

Applies Quality Control Robust Spline (QC-RSC) method to correct for signal drift and batch differences in mass spectrometry data.

Usage

sb_corr(
  order_col,
  batch_col,
  qc_col,
  smooth = 0,
  use_log = TRUE,
  min_qc = 4,
  qc_label = "QC",
  ...
)

Arguments

order_col	(character) The column name of sample_meta indicating the run order of the samples.
batch_col	(character) The column name of sample_meta indicating the batch each sample was measured in.
qc_col	(character) The column name of sample_meta indicating the group each sample is a member of.
smooth	(numeric) The amount of smoothing applied (0 to 1). If set to 0 the smoothing parameter will be estimated using leave-one-out cross-validation. The default is 0.
use_log	(logical) Log tranformation. Allowed values are limited to the following: "TRUE": The data is log transformed prior to performing signal correction. "FALSE": Signal correction is applied to the input data. The default is TRUE.
min_qc	(numeric) The minimum number of QC samples required for signal correction. The default is 4.
qc_label	(character) The label used to identify QC samples. The default is "QC".
...	Additional slots and values passed to struct_class.

Details

This object makes use of functionality from the following packages:

• pmp

Value

A sb_corr object.

struct object

References

Jankevics A, Weber RJM (2020). pmp: Peak Matrix Processing and signal batch correction for metabolomics datasets. R package version 1.1.0.

Kirwan JA, Broadhurst DI, Davidson RL, Viant MR (2013). “Characterising and correcting batch variation in an automated direct infusion mass spectrometry (DIMS) metabolomics workflow.” Analytical and Bioanalytical Chemistry, 405(15), 5147-5157.

Examples

M = sb_corr(order_col='run_order',batch_col='batch_no',qc_col='class')

structToolbox documentation built on Nov. 8, 2020, 6:54 p.m.