Extract isotope pattern for each feature.

[jorainer]

Define a function that helps identifying/subsetting a Spectra to extract the isotopes.

Have: one spectrum (i.e. a peak matrix with m/z and intensity values).
Want: indices of rows in the matrix that match isotopes (e.g. list(c(4, 5, 6), c(9, 10), c(23, 24, 25)) or c(NA, 1, 1, 1, NA, NA, 2, NA, 2, NA, NA, NA, 3, 3, 3, NA, NA), which would define the grouping of peaks into isotope groups).

Things to consider:

• single and double charged molecules.
• intensity of isotope peak must be smaller (at least by factor xxx) than main peak.

Approach:

• start with smallest m/z peak and iterate over all peaks in a spectrum (skipping the ones included in an isotope group).

[jorainer]

the m/z differences and expected signal proportion should be provided as a list or data.frame (columns mz and intensity). ideally there should be a function isotopes or similar that returns that data.frame and has a parameter to allow defining whether single or double charged ions are expected and other settings (number of isotopes?).

[jorainer]

TODOs:

• check also the Rdisop package how isotopes are defined there.
• evaluate other R packages that define isotopes.
• cross-check these with definitions provided by @vveri

[jorainer]

.isotope_peaks <- function(x, isotopeDefinition = isotopeDefinition()) {
}

#' @return `data.frame` with columns `mz` and `intensity`
isotopeDefinition <- function(charge = c(1L, 2L)) {
     data.frame(mz = c(1.0033, 0.99...), intensity = ....)
}