CorMID (version 0.3.1)

getMID: getMID.

Description

getMID will determine the measurable isotopic spectrum for a chemical formula.

Usage

getMID(
  fml,
  resolution = 20000,
  cutoff = 1e-04,
  isotopes = NULL,
  prec = 4,
  step = 0
)

Value

A two column matrix for mz and int values of the calculated spectrum.

Arguments

fml

Chemical formula.

resolution

Currently fixed to 20000 (might be made changeable in the future).

cutoff

Discard peaks below this threshold (relative to highest peak).

isotopes

Specify explicitly or keep NULL to use internally provided list.

prec

Rounding precision of returned mz and int values.

step

Can be used to return intermediate results (might be deprecated in the future).

Details

The computation yields similar results that would be obtained by packages `Rdisop` or `enviPat` but is completely in R (no C++ dependencies). However, it is approx. 7-fold slower than `Rdisop`. Where processing speed is of importance, please use the `algo` parameter of the `CorMID` function.

Examples

fml <- "C3H7Cl1"
getMID(fml)
if (FALSE) {
bench::mark(
 CorMID = dim(getMID(fml, prec=5)),
 Rdisop = dim(round(t(Rdisop::getMolecule(fml)$isotopes[[1]])[1:4,],5))
)
}

if (FALSE) {
data(chemforms, package = "enviPat")
chemforms <- chemforms[-grep("[[]", chemforms)]
bench::mark(
 CorMID = length(lapply(chemforms, getMID)),
 Rdisop = length(lapply(chemforms, Rdisop::getMolecule))
)
}