getAnalyticalInfo: Compose data block of MassBank record
In RMassBank: Workflow to process tandem MS files and build MassBank records

Description Usage Arguments Details Value Note Author(s) References See Also Examples

gatherCompound composes the data blocks (the "lower half") of all MassBank records for a compound, using the annotation data in the RMassBank options, spectrum info data from the analyzedSpec-type record and the peaks from the reanalyzed, multiplicity-filtered peak table. It calls gatherSpectrum for each child spectrum.

gatherCompound(spec, aggregated, additionalPeaks = NULL, retrieval="standard")

		gatherSpectrum(spec, msmsdata, ac_ms, ac_lc, aggregated, 
 		additionalPeaks = NULL, retrieval="standard")

`spec`	A `RmbSpectraSet` object, representing a compound with multiple spectra.
`aggregated`	An aggregate peak table where the peaks are extracted from.
`msmsdata`	A `RmbSpectrum2` object from the `spec` spectra set, representing a single spectrum to give a record.
`ac_ms, ac_lc`	Information for the AC\$MASS_SPECTROMETRY and AC\$CHROMATOGRAPHY fields in the MassBank record, created by `gatherCompound` and then fed into `gatherSpectrum`.
`additionalPeaks`	If present, a table with additional peaks to add into the spectra. As loaded with `addPeaks`.
`retrieval`	A value that determines whether the files should be handled either as "standard", if the compoundlist is complete, "tentative", if at least a formula is present or "unknown" if the only know thing is the m/z

The returned data blocks are in format list( "AC\$MASS_SPECTROMETRY" = list('FRAGMENTATION_MODE' = 'CID', ...), ...) etc.

gatherCompound returns a list of tree-like MassBank data blocks. gatherSpectrum returns one single MassBank data block or NA if no useful peak is in the spectrum.

Note that the global table additionalPeaks is also used as an additional source of peaks.

Michael Stravs

MassBank record format: http://www.massbank.jp/manuals/MassBankRecord_en.pdf

mbWorkflow, compileRecord

## Not run: 
     myspectrum <- w@spectra[[1]]
		massbankdata <- gatherCompound(myspectrum, w@aggregated)
		# Note: ac_lc and ac_ms are data blocks usually generated in gatherCompound and
		# passed on from there. The call below gives a relatively useless result :)
		ac_lc_dummy <- list()
		ac_ms_dummy <- list() 
		justOneSpectrum <- gatherSpectrum(myspectrum, myspectrum@child[[2]],
			ac_ms_dummy, ac_lc_dummy, w@aggregated)

## End(Not run)