mQTL.NMR (version 1.6.0)

segmentateSp: 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

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