GenerateMetaboliteSQLiteDB: GenerateMetaboliteSQLiteDB.

Description Usage Arguments Details Value Examples

Description

GenerateMetaboliteSQLiteDB will set up a SQLite data base containing potential metabolite formulas, their masses and isotopic distribution for use with InterpretMSSpectrum.

Usage

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GenerateMetaboliteSQLiteDB(dbfile = "SQLite_APCI.db", ionization = c("APCI",
  "ESI")[1], mass_range = c(80, 160), ncores = 2)

Arguments

dbfile

path and filename of the final SQLiteDB.

ionization

Has to be specified to account for different plausibility rules and elemental composition.

mass_range

For testing use default range, otherwise use your measurement range.

ncores

Number of cores. Use as many as possible.

Details

The process takes a long time for larger masses (>400 Da). Parallel processing with 8 cores is highly recommended. Alternatively pre-processed versions can be downloaded on request to jan.lisec@charite.de. To process a 1 Da range (from 900 to 901) for ESI does take ~5minutes on 8 cores.

Value

Returns NULL invisible. Will write an SQL_DB as specified by 'dbfile'.

Examples

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#this would be relatively fast, but for higher masses it is getting much slower

GenerateMetaboliteSQLiteDB(dbfile="APCI.db", ionization="APCI", mass_range=c(80,140), ncores=1)
GenerateMetaboliteSQLiteDB(dbfile="ESI.db", ionization="ESI", mass_range=c(900,901), ncores=8)

InterpretMSSpectrum documentation built on May 2, 2019, 11:05 a.m.