getAnnotationMat {metaMS} | R Documentation

## Obtain relative quantitative annotation results for GC-MS

### 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

[Package metaMS version 1.28.0 Index]