checkIsotopes {RMassBank} | R Documentation

## Checks for isotopes in a `msmsWorkspace`

### Description

Checks for isotopes in a `msmsWorkspace`

### Usage

    checkIsotopes(
      w,
      mode = "pH",
      intensity_cutoff = 0,
      intensity_precision = "none",
      conflict = "strict",
      isolationWindow = 2,
      evalMode = "complete",
      plotSpectrum = TRUE,
      settings = getOption("RMassBank")
    )

### Arguments

`w` | A `msmsWorkspace` to work with.
`mode` | `"pH", "pNa", "pM", "pNH4", "mH", "mM", "mFA"` for different ions ([M+H]+, [M+Na]+, [M]+, [M+NH4]+, [M-H]-, [M]-, [M+FA]-).
`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 `loadRmbSettings` et al. Refer to there for specific settings.

### Details

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.

### Value

The `msmsWorkspace` with annotated isolation peaks

### Author(s)

Michael Stravs, Eawag <michael.stravs@eawag.ch>

Erik Mueller, UFZ

[Package RMassBank version 3.0.0 Index]