gatherDataUnknown: Retrieve annotation data

In sneumann/RMassBank: Workflow to process tandem MS files and build MassBank records

Description

Retrieves annotation data for an unknown compound by using basic information present

Usage

gatherDataUnknown(id, mode, retrieval)

Arguments

id	The compound ID.
mode	"pH", "pNa", "pM", "pNH4", "mH", "mM", "mFA" for different ions ([M+H]+, [M+Na]+, [M]+, [M+NH4]+, [M-H]-, [M]-, [M+FA]-).
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

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 used to generate the data in case a substance is unknown, i.e. not enough information is present to derive anything about formulas or links

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

# Gather data for compound ID 131
## Not run: gatherDataUnknown(131,"pH")

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