segmentateSp {mQTL.NMR} | R Documentation

## Segmentation of a spectrum of interest

### Description

Determination of highly intensive peaks in the spectrum of interest and subsequent concatenation of closely located peaks into larger segments

### Usage

    segmentateSp(Sp, peakParam)

### Arguments

`Sp` | a vector defining the spectrum
`peakParam` | a list: ampThr: amplitude threshold [default 2*median(peaksMaxValues)] iFrameLen: Savitzky-Golay frame length iOrder: polynomial order of Savitzky - Golay filter iFrameLen: Savitzky-Golay frame length minPeakWidth: min peak size ppmDist: distance to concatenate adjacent peaks

### Value

A list:

`testSegmentsNew` | a list specifying the new test segments
`refSegmentsNew` | a list specifying the new reference segments

### Author(s)

Lyamine Hedjazi

### References

Veselkov,K. et al (2009) Recursive Segment-Wise Peak Alignment of Biological 1H NMR Spectra for Improved Metabolic Biomarker Recovery, Anal. Chem., 81(1), 56-66.

### See Also

`attachSegments`, `matchSegments`

### Examples

    ## Data
    load_datafiles()
    Sp<-t(read.table(phenofile))
    ppm<-as.numeric(colnames(Sp))

    ## Normalization
    normSp<-normalise(abs(Sp),'CS')

    ##Segmentation and matching parameters
    setupRSPA(ppm)

    ##reference spectrum selection
    attach(normSp)
    index<-selectRefSp(Sp,recursion$step)
    refSp<-Sp[index,]

    ##segmentate a reference spectrum
    refSegments<- segmentateSp(refSp, peakParam) # segmentate reference spectrum

[Package mQTL.NMR version 1.14.0 Index]