mergeMS: mergeMS
In mjhelf/MassTools: R package for mass and molecular formula calculations

Description Usage Arguments Details Value

Merge MS spectra, best used with noise-free spectra. Will merge all peaks that are EITHER within ppm OR within mzdiff range (mzdiff typically used to allow larger ppm difference in low mz range)

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mergeMS(speclist, ppm = 5, mzdiff = 5e-04, count = FALSE,
  iterative = T, removeZeros = T, noiselevel = 0, maxpeaks = NULL,
  toleranceFactor = 1)

`speclist`	list of spectra (matrices, all with two columns: `mz` and `intensity`)
`ppm`	min difference between peaks in ppm
`mzdiff`	min difference between peaks in m/z
`count`	if TRUE, will count how many peaks were combined into a peak, and add a `count` column in the resulting spectrum
`iterative`	if TRUE, will iteratively merge two adjacent peaks within tolerance, and then check if there are peaks within tolerance of merged peak
`removeZeros`	remove all entries with 0 intensity
`noiselevel`	all peaks below this intensity (relative to highest peak in merged spectrum at relative intensity 1) will be removed
`maxpeaks`	if not NULL, maximum number of peaks in merged spectrum. Lowest intensity peaks will be removed from merged spectrum.
`toleranceFactor`	should be a numeric vector of increasing values to recursively apply as a factor to the ppm and mzdiff tolerances.

Replacement for mergeMS(..., mergeOnly = T)

if speclist is a Spectra object or a list of Spectrum objects: returns a Spectrum object. if speclist is a matrix object or a list of matrix objects: returns a Spectrum object.