metIdentifyParam: Generate the parameter list for metIdentify function

View source: R/deprecated_metIdentify4all.R

metIdentifyParamR Documentation

Generate the parameter list for metIdentify function

Description

Generate the parameter list for metIdentify function. \lifecyclematuring

Usage

metIdentifyParam(
  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 = "all",
  column = c("hilic", "rp"),
  ms1.match.weight = 0.25,
  rt.match.weight = 0.25,
  ms2.match.weight = 0.5,
  total.score.tol = 0.5,
  candidate.num = 3,
  database,
  threads = 3
)

Arguments

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.

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

Value

A metIdentifyClass object.

Author(s)

Xiaotao Shen shenxt1990@163.com

See Also

The example and demo data of this function can be found https://jaspershen.github.io/metID/articles/multiple_databases.html

Examples

 param1 <-
metIdentifyParam(
  ms1.match.ppm = 15,
  rt.match.tol = 15,
  polarity = "positive",
  ce = "all",
  column = "rp",
  total.score.tol = 0.5,
  candidate.num = 3,
  threads = 3, 
  database = "msDatabase_rplc0.0.2"
)
param1

jaspershen/metID documentation built on July 31, 2022, 11:31 p.m.