signNorm: Normalize mass spectral data peak table

In WMBEdmands/MetMSLine: an automated and fully integrated pipeline for rapid processing of high-resolution LC-MS metabolomic datasets.

Description

normalizes mass spectral signal either by the median fold change (probabilistic quotient) or total ion signal methods

Usage

signNorm(peakTable = NULL, obsNames = NULL, method = "medFC")

Arguments

peakTable	either a data.frame, full file path as a character string to a .csv file of a peak table in the form observation (samples) in columns and variables (Mass spectral signals) in rows. If argument is not supplied a GUI file selection window will open and a .csv file can be selected.
obsNames	character vector of observation (i.e. sample/ QC/ Blank) names to identify appropriate observation (sample) columns.
method	either "medFC" for median fold change or "totIon" for total ion signal normalization. also a custom vector of factors equal in length to the obsNames argument with which to normalize the data can also be supplied. default = "medFC".

Value

a data frame identical to peakTable with samples normalized according to specificied method.

Source

http://www.ncbi.nlm.nih.gov/pubmed/21526840 Optimized preprocessing of ultra-performance liquid chromatography/mass spectrometry urinary metabolic profiles for improved information recovery.

WMBEdmands/MetMSLine documentation built on May 9, 2019, 10:03 p.m.