Generate the parameter list for identify_metabolites function

Generate the parameter list for metIdentify function.

identify_metabolites_params(
  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 or MS2 database.

threads

Number of threads

Value

A metIdentifyClass object.

See also

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

Author

Xiaotao Shen xiaotao.shen@outlook.com

Examples

 param1 <-
identify_metabolites_params(
  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"
)
#> This function is deprecated
param1
#> $metIdentifyParam
#> $metIdentifyParam$ms1.ms2.match.mz.tol
#> [1] 25
#> 
#> $metIdentifyParam$ms1.ms2.match.rt.tol
#> [1] 10
#> 
#> $metIdentifyParam$ms1.ms2.match.mz.tol
#> [1] 25
#> 
#> $metIdentifyParam$ms1.ms2.match.rt.tol
#> [1] 10
#> 
#> $metIdentifyParam$ms1.match.ppm
#> [1] 15
#> 
#> $metIdentifyParam$ms2.match.ppm
#> [1] 30
#> 
#> $metIdentifyParam$mz.ppm.thr
#> [1] 400
#> 
#> $metIdentifyParam$ms2.match.tol
#> [1] 0.5
#> 
#> $metIdentifyParam$fraction.weight
#> [1] 0.3
#> 
#> $metIdentifyParam$dp.forward.weight
#> [1] 0.6
#> 
#> $metIdentifyParam$dp.reverse.weight
#> [1] 0.1
#> 
#> $metIdentifyParam$rt.match.tol
#> [1] 15
#> 
#> $metIdentifyParam$polarity
#> [1] "positive"
#> 
#> $metIdentifyParam$ce
#> [1] "all"
#> 
#> $metIdentifyParam$column
#> [1] "rp"
#> 
#> $metIdentifyParam$ms1.match.weight
#> [1] 0.25
#> 
#> $metIdentifyParam$rt.match.weight
#> [1] 0.25
#> 
#> $metIdentifyParam$ms2.match.weight
#> [1] 0.5
#> 
#> $metIdentifyParam$total.score.tol
#> [1] 0.5
#> 
#> $metIdentifyParam$candidate.num
#> [1] 3
#> 
#> $metIdentifyParam$database
#> [1] "msDatabase_rplc0.0.2"
#> 
#> $metIdentifyParam$threads
#> [1] 3
#> 
#>