isowrap {enviPat}

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
)