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 |
ppm |
Should stick discretization be set in ppm ( |
dmz |
Stick discretization. Set to |
frac |
Used if |
env |
Peak shape function; either |
resolution |
Single resolution value or vector of resolutions with length equal to the number of entries in list |
plotit |
Should results be plotted, |
verbose |
Verbose, |
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
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
)
############################