rMSIannotation: rMSIannotation
In prafols/rMSIproc: MSI Processing in C++

Searches for isotopic ions in the peak matrix and evaluates them using morphology, intensity and mass error criteria. This algorithm only searches carbon-based isotopic ions. Using the infromation generated by the isotopes test, the algorithm then proceeds to search adduct pairs between the monoisotopic ions.

rMSIannotation(
  PeakMtx,
  iso.number = 2,
  iso.tolerance = 30,
  iso.charge = 1,
  iso.scoreThreshold = 0.75,
  iso.toleranceUnits = "ppm",
  iso.imageVector = NULL,
  addu.tolerance = 50,
  addu.adducts = data.frame(mass = c(38.963706, 22.98976, 1.007825), name = c("K",
    "Na", "H")),
  csv.results = FALSE,
  csv.path = getwd()
)

`PeakMtx`	List. An rMSIprocPeakMatrix. Must contain at least the following categories: PeakMtx$intensity. A matrix containg the intensities of the peaks for each pixel (rows = pixels, cols = ions). PeakMtx$mass. A vector containg the masses of each peak. Must be in the same order with the columns of the intensity marix. PeakMtx$numPixels. Number of pixels (rows in your matrix).
`iso.number`	Integer. Number of isotopes for each monoisotopic ion to be found.
`iso.tolerance`	Integer. Mass tolerance for the distance between isotope candidates in scans or ppms. (1.003355 Da +/- iso.tolerance)
`iso.charge`	Integer. Charge of the patterns to be found.
`iso.scoreThreshold`	Numeric between 0 and 1. ILS value to consider a pair of ions isotopes.
`iso.toleranceUnits`	String. The units of iso.tolerance. Must be 'ppm' or 'scan'. If ToleranceUnits is 'scan' then ImageVector must be the mass channels vector of the rMSI image (rMSIObj$mass).
`iso.imageVector`	Numeric Vector. The mass channels vector of the imaging dataset containing all the scans.
`addu.tolerance`	Integer. Mass error tolerance in ppm.
`csv.results`	Boolean. If TRUE, the annotations will be writen in CSV files under the name A.csv, B.csv and C.csv. By default FALSE.
`csv.path`	Path. Path to the folder where the CSV files shoul be stored. By default the working directory.
`addu.adductDataFrame`	Data frame containing the adducts to be searched. By defalut (+H, +Na and +K). It must have two columns. $name. Column containing the names as strings of the elements or molecules that form adducts (i.e. "Na", "K", "H") $mass. Masses of the adduct forming elements.

List.

$A: Data frame of the pairs of M+0 ions cataloged as adducts.
$B: Data frame of the pairs of M+0 ions and non-isotopic ions cataloged as adducts.
$C: Data frame of the all the M+0 ions.
$isotopicTestData: All the test results computed to determine the monoisotopic ions.
$monoisotopicPeaks: Peak matrix column indeces of monoisotopic peaks.
$isotopicPeaks: Peak matrix column indeces of isotopic peaks.