matchSamples2DB: Match pseudospectra from several samples to an in-house DB...

In yguitton/metaMS: MS-based metabolomics annotation pipeline

Match pseudospectra from several samples to an in-house DB (GC-MS)

Description

Compare experimental results to a database of pseudospectra. The result is a nested list, containing for every pseudospectrum in every sample either an index of a corresponding pattern in the DB (if a hit is found) or nothing (if no hit is found). Not meant to be called directly by the user.

Usage

matchSamples2DB(xset.msp, DB, settings, quick)

Arguments

xset.msp	An object containing a list of pseudospectra.
DB	The in-house database.
settings	The settings, in the form of a list.
quick	Logical. If TRUE, scaling of the pseudospectra (which is necessary for comparing to the database) will be done once using all masses in the pseudospectrum. This mode is routinely applied when comparing with a database of artefacts such as bleeding patterns or plasticizers. When comparing with a database of chemical standards, however, only peaks smaller than the molecular weight (+ 4, to allow for isotopes) should be taken into account in the scaling, and hence the scaling needs to be re-done for every comparison. This is _not_ so quick...

Value

A list object, with one element for each experimental sample. Every element again is a list with an entry for each pseudospectrum from that sample: if the element is empty, there is no match with the DB - a number points to the DB entry that gives a hit. Elements can contain more than one number; these will be split into one “best” annotation and “alternative” annotations in function annotations2tab.

Author(s)

Ron Wehrens

Examples

## Example of settings
  data(FEMsettings)
  metaSetting(object = TSQXLS.GC, field= "match2DB")

yguitton/metaMS documentation built on Feb. 27, 2023, 11:45 p.m.