constructExpPseudoSpectra: Create a list of all pseudospectra found in a GC-MS...

In rwehrens/metaMS: MS-based metabolomics annotation pipeline

Create a list of all pseudospectra found in a GC-MS experiment of several samples.

Description

Function constructExpPseudoSpectra creates an msp object containing all the patterns referenced to in the annotation. The first argument is the output of function matchSamples2Samples and contains the full annotation matrix and the pseudospectra of the known unknowns; the second is the msp object containing the standards that are actually found. Not meant to be called directly by the user.

Usage

constructExpPseudoSpectra(allMatches, standardsDB)

Arguments

allMatches	Result of a call to matchSamples2DB or matchSamples2Samples: a list containing the element annotation.
standardsDB	Database of standard spectra, in msp format.

Value

A list of spectra. All spectra from the database that are referenced to in the annotation slot will be present, and will be followed by all unknown spectra. In order to be able to see which patterns in the experimental data are pointing to which spectra, an extra slot DB.id is added, containing the position of the reference spectrum in the original database (which is what the numbers of the annotation object are referring to). Renumbering this is impractical since some patterns may be seen as alternative annotations, but may have no hits of their own - including them would lead to rows containing only zeros.

Author(s)

Ron Wehrens

See Also

matchSamples2DB, matchSamples2Samples

Examples

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

rwehrens/metaMS documentation built on Feb. 27, 2023, 5:13 a.m.