adductMatch.massdiff: Report closest-matching adduct type for a list of mass...
In kbseah/mass2adduct: Mass Spectrometry Imaging Molecular Adduct Finder

Description Usage Arguments Details Value See Also Examples

Given a set of mass differences produced by function massdiff, report for each pair of masses the closest-matching molecular transformation from a list of such potential adduct types. The built-in data sets adducts and adducts2 are examples of such lists of potential adducts.

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## S3 method for class 'massdiff'
adductMatch(x, add = mass2adduct::adducts, ppm = 2,
  mDa = NULL)

`x`	massdiff; Mass differences produced by `massdiff`
`add`	data.frame of adduct masses (default: "adducts" dataset in package)
`ppm`	numeric; the peak width (uncertainty) of the calculated peaks in proportional units, as parts per million (default: 2)
`mDa`	numeric; the peak width (uncertainty) of the calculated peaks in absolute mass units, as milliDaltons (default: NULL)

There are two options for setting a cutoff to match a given mass to a given potential adduct. The cutoff can be either proportional to the mass (and expressed as parts per million ppm) or a flat absolute value (in milliDaltons mDa). ppm is used by default. If a value for mDa is specified, then any value given to ppm is ignored. The ppm or mDa values are usually reported by the peak-picking software used.

Object of class massdiff, with additional element "matches" reporting the closest matches

adductMatch.massdiffhist gives an overview for large data sets by matching closest adducts to mass differences already binned into a histogram.

topAdducts to find the closest-matching adducts for the mass differences with the highest counts (the converse of the current function)

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d <- msimat(csv=system.file("extdata","msi.csv",package="mass2adduct"),sep=";")
d.diff <- massdiff(d) # Calculate mass differences from imported MSI data
d.diff.annotate <- adductMatch(d.diff,add=adducts2) # Report closest matches