isowrap: Combined (batch) calculation of isotope pattern, envelope and...
In enviPat: Isotope Pattern, Profile and Centroid Calculation for Mass Spectrometry

isowrap

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

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
)

enviPat documentation built on Oct. 21, 2022, 5:06 p.m.