peakdetection: An algorithm for the detection of peak locations and...

In dajofischer/cosmiq: cosmiq - COmbining Single Masses Into Quantities

Description

peakdetection uses Continuous wavelet transformation (CWT) to determine optimal peak location. A modified algorithm of Du et al. (2006) is used to localize peak positions.

Usage

    peakdetection(scales, y, x, SNR.Th, SNR.area, mintr)    

Arguments

scales	vector with the scales to perform CWT
y	vector of ion intensities
x	vector of mz bins
SNR.Th	Signal-to-noise threshold
SNR.area	Window size for noise estimation
mintr	Minimal peak width intensity treshold (in percentage), for which two overlapping peaks are considered as separated. default is set to 0.5.

Details

A peak detection algorithm based on continuous wavelet transformation (CWT) is used for this step (modified from Du et al., 2006). Peak detection based on CWT has the advantage that a sliding scale of wavelets instead of a single filter function with fixed wavelength is used. This allows for a flexible and automatic approximation of the peak width. As a result it is possible to locate both narrow and broad peaks within a given dynamic range.

Author(s)

David Fischer 2013

References

Du, P., Kibbe, W. A., & Lin, S. M. (2006). Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching. Bioinformatics, 22(17), 2059-2065. doi:10.1093/bioinformatics/btl355

Examples

    
cdfpath <- file.path(find.package("faahKO"), "cdf")

my.input.files <- dir(c(paste(cdfpath, "WT", sep='/'),
    paste(cdfpath, "KO", sep='/')), full.names=TRUE)


# create xcmsSet object
xs <- new("xcmsSet")
xs@filepaths <- my.input.files

op<-par(mfrow=c(3,1))

x<-combine_spectra(xs=xs, mzbin=0.25,
    linear=TRUE, continuum=FALSE)

plot(x$mz, x$intensity, 
    type='h', 
    main='original',
    xlab='m/Z', ylab='ion intensity')

xy <- peakdetection(x=x$mz, y=x$intensity,
    scales=1:10, SNR.Th=1.0, SNR.area=20, mintr=0.5)

id.peakcenter<-xy[,4]

plot(x$mz[id.peakcenter], x$intensity[id.peakcenter], type='h', 
    main='filtered')


plot(x$mz, x$intensity, type='l',
    xlim=c(400,450),
    main='zoom',
    log='y',
    xlab='m/Z', ylab='ion intensity (log scale)')

points(x$mz[id.peakcenter], x$intensity[id.peakcenter],col='red', type='h')
    

dajofischer/cosmiq documentation built on June 3, 2019, 6:21 p.m.