R: Finding Peaks in Raw Data

peaks {IDPmisc} | R Documentation

## Finding Peaks in Raw Data

### Description

Returns position, signal height and approximate width at half maximum peak height.

### Usage

    peaks(x, y = NULL, minPH, minPW, thr, stepF = 0.49)

### Arguments

`x, y` | Position and height of signal. Any reasonable way of defining the coordinates is acceptable. See function `link{getXY}` for details.
`minPH` | Mimimum height of peak to be reported.
`minPW` | Minimum width of peak at half maximum to be reported.
`thr` | Threshold below which the signal is not processed.
`stepF` | `StepF` defines indirectly the accuracy of the selection criteria `minPH` and `minPW` and of the value of the calculated width: The smaller the more accurate and the slower the function. It must be <0.5

### Details

The function is especially useful for signals in which both very broad and very narrow peaks are of interest. The peaks may lie very close to each other or might even be superpositioned on top of each other, e.g. peaks on broader shoulders. The algorithm is also very useful when the resolution of the signal is poor and the noise is small.

The function is looking for peaks without any preceding baseline substraction or smoothing, which could distort the spectrum.

The selection criteria `minPH` and `minPW` and the values for the calculated peak widths are only approximate.

### Value

dataframe consisting of

`x` | Position of peak
`y` | Signal height
`w` | Approximate width at half maximum of peak

### Note

In the function, the main selection criterium for the peaks is the height of the peaks, the second optional criterium is the width of the peaks.

### Author(s)

Rene Locher

### Examples

    n <- 200
    freq <- 1:n
    theory <- sin(freq/n*4*pi)*cos(freq/n*3*pi)
    spec <- theory + 0.1*rnorm(n)

    plot(spec,type="b")
    lines(theory,lwd=2)

    pts <- peaks(spec, minPH=0.7)
    points(pts,col="red",cex=1.2, pch=20)

    ## peaks after smoothing the spectrum
    spec.sm <- loess.smooth(freq, spec, span=0.2,
                            degree = 2, evaluation = 100)
    lines(spec.sm$x, spec.sm$y, col="steelblue", lwd=2)
    pts <- peaks(spec.sm, minPH=0.4)
    points(pts,col="green",cex=1.2,pch=20)

    ## Analyses of Mass Spectrum between 12000 and 100'000
    ## without smoothing, without baseline substraction
    data(MS)
    MS1 <- log10(MS[MS$mz>12000&MS$mz<1e5,])

    P <- peaks(MS1, minPH=0.02, minPW=0.001)
    plot(MS1, type="l", xlab="log10(mz)", ylab="log10(I)")
    points(P,col="blue",cex=1.6)

[Package IDPmisc version 1.1.20 Index]