matching-funs: Functions to match a peak-intensity table to KEGG database
In b2slab/mWISE: Untargeted LC-MS data annotation

Description Usage Arguments Value Examples

Function mass.range.format builds mz ranges for a peak-intensity table using mz.ppm.converter if required.

Function matchingStage performs a fast matching of the peak-intensity table to KEGG database using adducts and fragments knowledge.

Function mz.ppm.converter transforms the user-defined tolerance from ppm to mz uncertainty or viceversa.

mass.range.format(
  Peak.List,
  force.mass.range = TRUE,
  mass.range.type = "ppm.mode",
  mz.range,
  ppm = 10
)

matchingStage(
  Peak.List,
  force.mass.range = TRUE,
  mass.range.type = "ppm.mode",
  mz.range = NULL,
  ppm = 10,
  polarity = "positive",
  Add.List = NULL,
  Cpd.Add,
  do.Par = TRUE,
  nClust = 2
)

mz.ppm.converter(
  tol = 10,
  mzrange = 0.001,
  mz,
  conversion = c("ppm.to.mz", "mz.to.ppm")
)

`Peak.List`	Data frame containing the LC-MS features. Columns should contain: Peak.Id for a peak identifier mz for a mass-to-charge ratio value rt for the retention time Intensities for each sample
`force.mass.range`	Logical. If TRUE, the m/z range is computed using the user-defined ppm tolerance or mz.range (Def: TRUE).
`mass.range.type`	A character indicating if the m/z range computation is performed using tolerance in ppm ("ppm.mode"). or m/z uncertainty ("mz.range") (Def: "ppm.mode").
`mz.range`	If mass.range.type = "mz.range", it indicates the m/z range uncertainty (i.e. mz.range = 0.001).
`ppm`	If mass.range.type = "ppm.mode", it indicates the tolerance in ppm (i.e. ppm = 10).
`polarity`	Acquisition mode of the study. It can be "positive" or "negative".
`Add.List`	List of adducts or fragments to consider.
`Cpd.Add`	Compound to adduct matrix. It can be built using `CpdaddPreparation` function. If NULL, the default information will be used.
`do.Par`	Logical. If parallel computing is required (Def: TRUE).
`nClust`	Number of clusters that may be used (Def: 2)
`tol`	Tolerance in ppm. Def: 10
`mzrange`	mz uncertainty. Def: 0.001
`mz`	mass-to-charge ratio for which the conversion is performed.
`conversion`	Direction of the conversion. Character vector containing some of: "ppm.to.mz", "mz.to.ppm"

Function mass.range.format returns the input peak list with two additional columns containing the mzmin and mzmax values.

Function matchingStage returns a list containing the input peak list and the table of annotated peaks, containing all the potential KEGG candidates for each LC-MS feature.

Function mz.ppm.converter returns a vector of values containing uncertainty (if conversion="ppm.to.mz") or tolerance in ppm (if conversion="mz.to.ppm")

data("sample.keggDB")
Cpd.Add <- CpdaddPreparation(KeggDB = sample.keggDB, 
do.Par = FALSE)
data(sample.dataset)
Peak.List <- sample.dataset$Positive$Input
Annotated.List <- matchingStage(Peak.List = Peak.List, 
                                Cpd.Add = Cpd.Add,
                                polarity = "positive", 
                                do.Par = FALSE)