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

View source: R/matchSamples2DB.R

matchSamples2DBR Documentation

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


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.


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



An object containing a list of pseudospectra.


The in-house database.


The settings, in the form of a list.


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...


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.


Ron Wehrens


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

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