searchMZ: Find matches for m/z value in given database

In MetaDBparse: Annotate Mass over Charge Values with Databases and Formula Prediction

Description

This function takes user m/z, ppm error, base database and the extended database to return hits of interest.

Usage

searchMZ(
  mzs,
  ionmodes,
  outfolder,
  base.dbname,
  ppm,
  ext.dbname = "extended",
  append = FALSE
)

Arguments

mzs	Vector of m/z values
ionmodes	Vector of pos/negative mode for each m/z value
outfolder	Which folder are your databases stored in?
base.dbname	Which base database do you want to retrieve info from? (without .db suffix)
ppm	Parts per million accepted error range
ext.dbname	Name of extended database (without .db suffix), Default: 'extended'
append	Use this when searching muiltiple base databases, so only one result table is created, Default: FALSE

Value

Data table with match results

See Also

SQLite rbindlist dbExecute,dbGetQuery,dbDisconnect fn

Examples

 ## Not run: myFolder = tempdir()
 ## Not run: buildBaseDB(outfolder = myFolder, "lmdb", test = TRUE)
 ## Not run: file.remove(file.path(myFolder, "extended.db"))
 ## Not run: data(adducts)
 ## Not run: data(adduct_rules)
 ## Not run: buildExtDB(outfolder = myFolder, base.dbname = "lmdb",
 silent=FALSE, adduct_table = adducts, adduct_rules = adduct_rules)
## End(Not run)
 ## Not run: searchMZ(c("104.3519421"), "positive", outfolder = myFolder, "lmdb", ppm = 3)

MetaDBparse documentation built on May 3, 2021, 5:09 p.m.