R: Combined (batch) calculation of isotope pattern, envelope and...

isowrap {enviPat} | R Documentation

## Combined (batch) calculation of isotope pattern, envelope and centroids/intensoids/valleys on interpolated resolutions.

### Description

Wrapper combining the functions `getR`, `isopattern`, `envelope` and `vdetect`.

Uses chemical formulas from `check_chemform` as argument.

### Usage

    isowrap(isotopes, checked, resmass, resolution = FALSE, nknots = 6,
    spar = 0.2, threshold = 0.1, charge = 1, emass = 0.00054858, algo=2,
    ppm = FALSE, dmz = "get", frac = 1/4, env = "Gaussian",
    detect = "centroid", plotit = FALSE)

### Arguments

`isotopes` | Dataframe listing all relevant isotopes, such as `isotopes`.
`checked` | Output dataframe from `check_chemform` with correct chemical formulas.
`resmass` | For resolution interpolation: dataframe with two columns, resolution and mass; see `getR`. Otherwise, set to `FALSE` and use argument `resolution` to utilize a single resolution.
`resolution` | Single resolution value. Only used if argument `resmass` is set to `FALSE`.
`nknots` | Number of knots, see `getR`. Ignored if argument `resmass` set to `FALSE`.
`spar` | Smoothing parameter, see `getR`. Ignored if argument `resmass` set to `FALSE`.
`threshold` | Abundance below which isotope peaks are omitted, see `isopattern`.
`charge` | z in m/z, see `isopattern`.
`emass` | Electrone mass. Only relevant if `charge` is not set to `FALSE`, see `isopattern`.
`algo` | Which algorithm to use? Type `1` or `2`. See details section in `isopattern`.
`ppm` | Set stick discretization, see details section of `envelope`.
`dmz` | Set stick discretization, see details section of `envelope`.
`frac` | Set stick discretization, see details section of `envelope`.
`env` | Peak shape function, see `envelope`.
`detect` | Return either `"centroid"`, `"intensoid"` or `"valley"`. See `vdetect`.
`plotit` | Should results be plotted, `TRUE/FALSE`?

### Value

List with length equal to length of list `profiles`, with equal names of list entries. Each entry in that list contains the centroids, intensoids or valley of the envelope in two columns:

`m/z` | m/z
`abundance` | area(centroid) or abundance (intensoid, valley)

### Author(s)

Martin Loos, Christian Gerber

### See Also

`vdetect`

### Examples

    data(isotopes);
    data(resolution_list);
    data(chemforms);
    chemforms<-chemforms[1:10];

    checked<-check_chemform(
        isotopes,
        chemforms
      );

    resmass<-resolution_list[[1]]

    centro<-isowrap(
      isotopes,
      checked,
      resmass=resolution_list[[4]],
      resolution=FALSE,
      nknots=4,
      spar=0.2,
      threshold=0.1,
      charge=1,
      emass=0.00054858,
      algo=2,
      ppm=FALSE,
      dmz="get",   # retrieve dm from R=m/dm
      frac=1/4,
      env="Gaussian",
      detect="centroid",
      plotit=TRUE
    )

[Package enviPat version 2.4 Index]