R: Isotope pattern envelope calculation

envelope {enviPat} | R Documentation

## Isotope pattern envelope calculation

### Description

Convolutes an isotope pattern from `isopattern` with a peak shape function (Gaussian or Cauchy-Lorentz function) to its theoretical envelope (profile), at a given measurement resolution. The envelope is represented by sticks, i.e. measurement abundances at discrete m/z intervals.

### Usage

    envelope(pattern, ppm = FALSE, dmz = "get", frac = 1/4, env = "Gaussian",
    resolution = 5e+05, plotit = FALSE, verbose = TRUE)

### Arguments

`pattern` | List of isotope pattern(s) as generated by `isopattern`.
`ppm` | Should stick discretization be set in ppm (`TRUE`) or absolute m/z (`FALSE`)? Only checked if `dmz` is not set to `"get"`; check details section.
`dmz` | Stick discretization. Set to `"get"` to derive discretization from argument `resolution` or set a numerical value in combination with `ppm` to use as ppm or absolute m/z. Check details section.
`frac` | Used if `dmz` is set to `"get"`. Check details section.
`env` | Peak shape function; either `"Gaussian"` or `"CauchyLorentz"`.
`resolution` | Single resolution value or vector of resolutions with length equal to the number of entries in list `pattern`. Check resolution definition in the details section.
`plotit` | Should results be plotted, `TRUE/FALSE` ?
`verbose` | Verbose, `TRUE/FALSE`?

### Details

The theoretical profiles are represented by sticks, i.e. abundances at discrete m/z intervals. While the profile width is set by argument `resolution`, the mass discretization between adjacent sticks can be set in two different ways.

On the one hand, discretization can be given as a numerical value, either in ppm or absolute m/z. To do so, set argument `dmz` to a numerical value and specify with argument `ppm` if this value is stating the discretization in ppm or as absolute m/z.

On the other hand, discretization can be derived from the measurement resolution (R) set by argument `resolution`. To do so, set `dmz` to `"get"`, which leads to argument `ppm` being ignored. In this case, the stick discretization is retrieved from (dm/z)*`frac`, with (dm/z) = (m/z)/R = peak width at half maximum.

### Value

List with length equal to length of list `pattern`, with equal names of list entries. Each entry in that list contains the sticks of the envelope in two columns:

`m/z` | Stick m/z
`abundance` | Stick abundance

### Note

The resolution R is defined as R=(m/z)/(dm/z), with dm/z = peak width at half maximum, cp. `resolution_list`.

### Author(s)

Martin Loos, Christian Gerber

### References

Li, L., Kresh, J., Karabacak, N., Cobb, J., Agar, J. and Hong, P. (2008). A Hierarchical Algorithm for Calculating the Isotopic Fine Structures of Molecules. Journal of the American Society for Mass Spectrometry, 19, 1867–1874.

### See Also

`isopattern` `getR` `vdetect`

### Examples

    ############################
    # batch of chemforms #######
    data(isotopes)
    data(chemforms)
    chemforms<-chemforms[1:5]

    pattern<-isopattern(
      isotopes,
      chemforms,
      threshold=0.1,
      plotit=TRUE,
      charge=FALSE,
      emass=0.00054858,
      algo=2
    )

    profiles<-envelope(
        pattern,
        ppm=FALSE,
        dmz=0.0001,
        frac=1/4,
        env="Gaussian",
        resolution=1E6,
        plotit=TRUE
    )
    ############################

[Package enviPat version 2.4 Index]