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]