segmentateSp: Segmentation of a spectrum of interest

In lhedjazi/mQTL.NMR: Metabolomic Quantitative Trait Locus Mapping for 1H NMR data

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

lhedjazi/mQTL.NMR documentation built on May 31, 2019, 10:47 p.m.