metABM: metABM
In ZhuMSLab/MetDNA: MetDNA

metABM

R Documentation

metABM

Description

Annotate peaks based on metabolic reaction network (MRN).

Usage

metABM(annotation.result = "ms2.match.annotation.result.csv",
  ms2.data = "ms2", prefer.adduct = c("all", "M+H", "M+Na", "M-H"),
  use.default.md = TRUE, column = c("hilic", "rp"),
  polarity = c("positive", "negative"), threads = 3, path = file.path(".",
  "MS2_match_result"), output.path = file.path(".", "MRN_annotation_result"),
  max.isotope = 4, mz.tol = 25, rt.tol1 = 3, rt.tol2 = 30,
  cor.tol = 0, int.tol = 500, dp.tol = 0.5, max.step = 3,
  score.cutoff = 0, remain = FALSE, remain.per = 0.5,
  seed.neighbor.match.plot = FALSE, candidate.num = 3)

Arguments

`annotation.result`	The name of annotation result from ms2Annotation.
`ms2.data`	The name of ms2 data from ms2Annotation.
`prefer.adduct`	Which adduct you want to use for RT prediction.
`use.default.md`	Use default molecular descriptors for RT prediction or not.
`column`	hilic or rp.
`polarity`	positive or negative.
`threads`	The number of threads.
`path`	The work directory.
`output.path`	The directory for output results.
`max.isotope`	The number of isotope peaks
`mz.tol`	The m/z tolerance. Default is 25 ppm.
`rt.tol1`	The RT tolerance for isotope and adduct annotation. (second) Default is 3.
`rt.tol2`	The RT tolerance for metabolite annotation. (%) Default is 30%.
`cor.tol`	The correlation tolerance.
`int.tol`	The intensity ratio tolerance of isotope annotation.
`dp.tol`	The tolerance of dot product.
`max.step`	The max number of reaction step.
`score.cutoff`	Score cutoff of annotations.
`remain`	Remain some seeds as validation or not.
`remain.per`	The percentage of remained seeds. Default is 50%.
`seed.neighbor.match.plot`	Output MS/MS match plot of seed and neighbor or not.
`candidate.num`	How many candidates for peaks are outputted. Default is 3.