flatten: Flatten, or re-read, MassBank header blocks
In sneumann/RMassBank: Workflow to process tandem MS files and build MassBank records

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

flatten converts a list of MassBank compound information sets (as retrieved by gatherData) to a flat table, to be exported into an infolist. readMbdata reads a single record from an infolist flat table back into a MassBank (half-)entry.

1
2
3

flatten(mbdata) 

readMbdata(row)

`mbdata`	A list of MassBank compound information sets as returned from `gatherData`.
`row`	One row of MassBank compound information retrieved from an infolist.

Neither the flattening system itself nor the implementation are particularly fantastic, but since hand-checking of records is a necessary evil, there is currently no alternative (short of coding a complete GUI for this and working directly on the records.)

flatten returns a matrix (not a data frame) to be written to CSV.

readMbdata returns a list of type list(id= compoundID, ..., 'ACCESSION' = '', 'RECORD_TITLE' = '', ) etc.

Michael Stravs

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

gatherData,loadInfolist

## Not run: 
	# Collect some data to flatten
	ids <- c(40,50,60,70)
 data <- lapply(ids, gatherData)
 # Flatten the data trees to a table
 flat.table <- flatten(data)
 # reimport the table into a tree
 data.reimported <- apply(flat.table, 1, readMbdata)

## End(Not run)