toMassbank {RMassBank} | R Documentation |
Writes a MassBank record in list format to a text array.
toMassbank(mbdata)
mbdata |
A MassBank record in list format. |
The function is a general conversion tool for the MassBank format; i.e. the
field names are not fixed. mbdata
must be a named list, and the
entries can be as follows:
A single text line:
'CH\$EXACT_MASS' = '329.1023'
is written as
CH\$EXACT_MASS: 329.1023
A character array:
'CH\$NAME' = c('2-Aminobenzimidazole', '1H-Benzimidazol-2-amine')
is written as
CH\$NAME: 2-Aminobenzimidazole
CH\$NAME: 1H-Benzimidazol-2-amine
A named list of strings:
'CH\$LINK' = list('CHEBI' = "27822", "KEGG" = "C10901")
is written as
CH\$LINK: CHEBI 27822
CH\$LINK: KEGG C10901
A data frame (e.g. the peak table) is written as specified in the MassBank record format (Section 2.6.3): the column names are used as headers for the first line, all data rows are printed space-separated.
The result is a text array, which is ready to be written to the disk as a file.
The function iterates over the list item names. This means that
duplicate entries in mbdata
are (partially) discarded! The correct
way to add them is by making a character array (as specified above): Instead
of 'CH\$NAME' = 'bla', 'CH\$NAME' = 'blub'
specify 'CH\$NAME' =
c('bla','blub')
.
Michael Stravs
MassBank record format: http://www.massbank.jp/manuals/MassBankRecord_en.pdf
compileRecord
, mbWorkflow
## Not run: # Read just the compound info skeleton from the Internet for some compound ID id <- 35 mbdata <- gatherData(id) #' # Export the mbdata blocks to line arrays # (there is no spectrum information, just the compound info...) mbtext <- toMassbank(mbdata) ## End(Not run)