RMassBank (version 2.0.0)

flatten: Flatten, or re-read, MassBank header blocks

Description

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.

Usage

flatten(mbdata) 
readMbdata(row)

Arguments

mbdata

A list of MassBank compound information sets as returned from gatherData.

row

One row of MassBank compound information retrieved from an infolist.

Value

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.

Details

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.)

References

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

See Also

gatherData,loadInfolist

Examples

## 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)