dot-buildRecord.RmbSpectraSet: Compile MassBank records
In sneumann/RMassBank: Workflow to process tandem MS files and build MassBank records

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

Takes a spectra block for a compound, as returned from analyzeMsMs, and an aggregated cleaned peak table, together with a MassBank information block, as stored in the infolists and loaded via loadInfolist/readMbdata and processes them to a MassBank record

1	compileRecord(spec, mbdata, aggregated, additionalPeaks = NULL, retrieval="standard")

`mbdata`	The information data block for the record header, as stored in `mbdata_relisted` after loading an infolist.
`additionalPeaks`	If present, a table with additional peaks to add into the spectra. As loaded with `addPeaks`.
`spec`	A `RmbSpectraSet` for a compound, after analysis (`analyzeMsMs`). Note that peaks are not read from this object anymore: Peaks come from the `aggregated` dataframe (and from the global `additionalPeaks` dataframe; cf. `addPeaks` for usage information.)
`aggregated`	An aggregated peak data table containing information about refiltered spectra etc.
`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

compileRecord calls gatherCompound to create blocks of spectrum data, and finally fills in the record title and accession number, renames the "internal ID" comment field and removes dummy fields.

Returns a MassBank record in list format: e.g. list("ACCESSION" = "XX123456", "RECORD_TITLE" = "Cubane", ..., "CH\$LINK" = list( "CAS" = "12-345-6", "CHEMSPIDER" = 1111, ...))

Michael Stravs

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

mbWorkflow, addPeaks, gatherCompound, toMassbank

#
## Not run: myspec <- w@spectra[[2]]
# after having loaded an infolist:
## Not run: mbdata <- mbdata_relisted[[which(mbdata_archive\$id == as.numeric(myspec\$id))]]
## Not run: compiled <- compileRecord(myspec, mbdata, w@aggregated)

sneumann/RMassBank documentation built on Oct. 20, 2020, 3:19 p.m.