matchSamples2Samples matches pseudospectra across all
samples - if a pseudospectrum is present at more or less the same
retention time in several samples, it can get the status of
“unknown”. Exactly how much difference there may be between the
pseudospectra and retention times, and how often it should be present,
is determined by the settings. The auxiliary function
match.unannot.patterns compares two msp objects, representing
experimental samples. Both are not meant to be called directly by the
user.matchSamples2Samples(xset.msp.scaled, xset.msp, annotations, settings)
match.unannot.patterns(msp1, msp2, settings)FEMsettings,
field matchIrrelevants.matchSamples2Samples returns an updated
annotation object such as the one
returned by matchSamples2DB, but now with an additional
unknowns element, containing the pseudospectra that are
recognized as “unknowns”.Function match.unannot.patterns returns a list of combinations
of pseudospectra IDs, retention times (or retention indices) and match
factors (only for those combinations that satisfy the criteria on
retention time (index) and match factor).