getAnnotationMat: Obtain relative quantitative annotation results for GC-MS

In metaMS: MS-based metabolomics annotation pipeline

Description

Function getAnnotationMat obtains relative intensities for features in individual samples. A robust linear regression is performed when the number of common features is five or larger; for 2-4 peaks a weighted linear regression is used, and if only one peak is in common the intensity ratio for this peak is used. Reference patterns are the patterns in the database of standards or the patterns in the “unknowns” element of the allMatches object. Not meant to be called directly by the user.

Usage

getAnnotationMat(exp.msp, pspectra, allMatches)
relInt(pat, refpat)

Arguments

exp.msp	List of experimental pseudospectra.
pspectra	Spectra from the in-house database.
allMatches	Match information in the form of a list.
pat, refpat	Both pseudospectra.

Value

Function getAnnotationMat returns a matrix containing all patterns (standards as well as unknowns) in the rows, and numeric values signifying relative intensities in all samples in the columns. These relative intensities are the quantities calculated by relInt, which simply returns one number.

Author(s)

Ron Wehrens

Examples

## Example of results
  data(GCresults) ## pre-compiled results
  GCresults$PeakTable

metaMS documentation built on Nov. 8, 2020, 8:21 p.m.