checkIsotopes {RMassBank} | R Documentation |
msmsWorkspace
Checks for isotopes in a msmsWorkspace
checkIsotopes( w, mode = "pH", intensity_cutoff = 0, intensity_precision = "none", conflict = "strict", isolationWindow = 2, evalMode = "complete", plotSpectrum = TRUE, settings = getOption("RMassBank") )
w |
A |
mode |
|
intensity_cutoff |
The cutoff (as an absolute intensity value) under which isotopic peaks shouldn't be checked for or accepted as valid. Please note: The cutoff is not hard in the sense that it interacts with the intensity_precision parameter. |
intensity_precision |
The difference that is accepted between the calculated and observed intensity of a possible isotopic peak. Further details down below. |
conflict |
Either "isotopic"(Peak formulas are always chosen if they fit the requirements for an isotopic peak) or "strict"(Peaks are only marked as isotopic when there hasn't been a formula assigned before.) |
isolationWindow |
Half of the width of the isolation window in Da |
evalMode |
Currently no function yet, but planned. Currently must be "complete" |
plotSpectrum |
A boolean specifiying whether the spectrumshould be plotted |
settings |
Options to be used for processing. Defaults to the options loaded via
|
text describing parameter inputs in more detail.
intensity_precision
This parameter determines how strict the intensity values should adhere to the calculated intensity in relation to the parent peak.
Options for this parameter are "none"
, where the intensity is irrelevant, "low"
, which has an error margin of 70% and "high"
, where the error margin
is set to 35%. The recommended setting is "low"
, but can be changed to adjust to the intensity precision of the mass spectrometer.
The msmsWorkspace
with annotated isolation peaks
Michael Stravs, Eawag <michael.stravs@eawag.ch>
Erik Mueller, UFZ