metIdentify: metIdentify
In jaspershen/metIdentify: Metabolite identification based on MS1 and MS2 spectra

Description Usage Arguments Value Author(s) See Also

Identify metabolites based on MS/MS database.

metIdentify(ms1.data, ms2.data, ms1.ms2.match.mz.tol = 25,
  ms1.ms2.match.rt.tol = 10, ms1.match.ppm = 25, ms2.match.ppm = 30,
  mz.ppm.thr = 400, ms2.match.tol = 0.5, fraction.weight = 0.3,
  dp.forward.weight = 0.6, dp.reverse.weight = 0.1,
  rt.match.tol = 30, polarity = c("positive", "negative"), ce = "30",
  column = c("hilic", "rp"), ms1.match.weight = 0.25,
  rt.match.weight = 0.25, ms2.match.weight = 0.5, path = ".",
  total.score.tol = 0.5, candidate.num = 3, database, threads = 3)

`ms1.data`	The name of ms1 peak table (csv format). Column 1 is "name", Column 2 is "mz" and column is "rt" (second).
`ms2.data`	MS2 data, must be mgf, msp or mzXML format. For example, ms2.data = c("test.mgf", "test2.msp").
`ms1.ms2.match.mz.tol`	MS1 peak and MS2 spectrum matching m/z tolerance. Default is 25 pm.
`ms1.ms2.match.rt.tol`	MS1 peak and MS2 spectrum matching RT tolerance. Default is 10 s.
`ms1.match.ppm`	Precursor match ppm tolerance.
`ms2.match.ppm`	Fragment ion match ppm tolerance.
`mz.ppm.thr`	Accurate mass tolerance for m/z error calculation.
`ms2.match.tol`	MS2 match (MS2 similarity) tolerance.
`fraction.weight`	The weight for matched fragments.
`dp.forward.weight`	Forward dot product weight.
`dp.reverse.weight`	Reverse dot product weight.
`rt.match.tol`	RT match tolerance.
`polarity`	The polarity of data, "positive"or "negative".
`ce`	Collision energy. Please confirm the CE values in your database. Default is "all".
`column`	"hilic" (HILIC column) or "rp" (reverse phase).
`ms1.match.weight`	The weight of MS1 match for total score calculation.
`rt.match.weight`	The weight of RT match for total score calculation.
`ms2.match.weight`	The weight of MS2 match for total score calculation.
`path`	Work directory.
`total.score.tol`	Total score tolerance. The total score are refering to MS-DIAL.
`candidate.num`	The number of candidate.
`database`	MS2 database name.
`threads`	Number of threads