gatherDataBabel: Retrieve annotation data

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

View source: R/createMassBank.R

Description

Retrieves annotation data for a compound by using babel, based on the SMILES code and name of the compounds stored in the compound list.

Usage

1

Arguments

id

The compound ID.

Details

Composes the "upper part" of a MassBank record filled with chemical data about the compound: name, exact mass, structure, CAS no.. The instrument type is also written into this block (even if not strictly part of the chemical information). Additionally, index fields are added at the start of the record, which will be removed later: id, dbcas, dbname from the compound list.

Additionally, the fields ACCESSION and RECORD_TITLE are inserted empty and will be filled later on.

This function is an alternative to gatherData, in case CTS is down or if information on one or more of the compounds in the compound list are sparse

Value

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

Author(s)

Michael Stravs, Erik Mueller

References

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

See Also

mbWorkflow

Examples

1
2
# Gather data for compound ID 131
## Not run: gatherDataBabel(131)

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