R: Finds monoisotopic peaks in a MassPeaks object.
monoisotopicPeaks-methods
R Documentation
Finds monoisotopic peaks in a MassPeaks object.
Description
This method looks for monoisotopic peaks in peak list data
(represented by a MassPeaks objects).
It is based on the poisson model for isotopic patterns described in Breen et al
2000.
Usage
## S4 method for signature 'MassPeaks'
monoisotopicPeaks(object,
minCor=0.95, tolerance=1e-4, distance=1.00235, size=3L:10L)
## S4 method for signature 'list'
monoisotopicPeaks(object, ...)
Arguments
object
MassPeaks object or a list of
MassPeaks objects.
minCor
double, minimal correlation between the peak pattern
generated by the model and the experimental peaks in the
MassPeaks object to be recognized as isotopic pattern.
tolerance
double, maximal relative deviation of peaks
position (mass) to be considered as isotopic distance (
abs(((mass[i]+distance)-mass[i+1])/mass[i]) < tolerance).
distance
double, distance between two consecutive peaks in an
isotopic pattern (default value taken from Park et al 2008). Could contain
more than one value, e.g. distance=(1:3)^-1 to find isotopic
patterns for multiple charged patterns (e.g. 1+, 2+, and 3+). Please note
that the order matters here if there is a monoisotopic peak for charge
state 1 and 3 it would be reported as charge 1 for
distance=(1:3)^-1 and as 3 for distance=(3:1)^-1
respectively.
size
double, size (length) of isotopic pattern, longer patterns
are prefered over shorter ones.
...
arguments to be passed to
monoisotopicPeaks,MassPeaks-method. If
object is a listmc.cores is also supported.
Value
Returns a MassPeaks object with monoisotopic peaks only.
K. Park, J.Y. Yoon, S. Lee, E. Paek, H. Park, H.J. Jung, and S.W. Lee. 2008.
Isotopic peak intensity ratio based algorithm for determination of isotopic
clusters and monoisotopic masses of polypeptides from high-resolution
mass spectrometric data.
Analytical Chemistry, 80: 7294-7303.
E.J. Breen, F.G. Hopwood, K.L. Williams, and M.R. Wilkins. 2000.
Automatic poisson peak harvesting for high throughput protein identification.
Electrophoresis 21: 2243-2251.
## load package
library("MALDIquant")
## create example peaks
p <- createMassPeaks(mass=995:1005,
intensity=c(100, 10, 30, 10, 40, # noise
550, 330, 110, 10, # isotopic pattern
5, 15)) # more noise
m <- monoisotopicPeaks(p)
as.matrix(m)
## plot the peaks and mark the monoisotopic one
plot(p)
points(m, col=2, pch=4)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(MALDIquant)
This is MALDIquant version 1.15
Quantitative Analysis of Mass Spectrometry Data
See '?MALDIquant' for more information about this package.
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MALDIquant/monoisotopicPeaks-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: monoisotopicPeaks-methods
> ### Title: Finds monoisotopic peaks in a MassPeaks object.
> ### Aliases: monoisotopicPeaks monoisotopicPeaks,MassPeaks-method
> ### monoisotopicPeaks,list-method
> ### Keywords: methods
>
> ### ** Examples
>
> ## load package
> library("MALDIquant")
>
> ## create example peaks
> p <- createMassPeaks(mass=995:1005,
+ intensity=c(100, 10, 30, 10, 40, # noise
+ 550, 330, 110, 10, # isotopic pattern
+ 5, 15)) # more noise
> m <- monoisotopicPeaks(p)
> as.matrix(m)
mass intensity
[1,] 1000 550
>
> ## plot the peaks and mark the monoisotopic one
> plot(p)
> points(m, col=2, pch=4)
>
>
>
>
>
> dev.off()
null device
1
>