segmentateSp: Segmentation of a spectrum of interest

In mQTL: Metabolomic Quantitative Trait Locus Mapping

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	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	new test segments
refSegmentsNew	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

Sp=matrix(rnorm(10*13454,mean=0,sd=1), nrow=10,ncol=13454)

##Segmentation parameters

peakParam=list()
peakParam$ppmDist <- 0.03# (ppm)  # distance to concatenate adjacent peaks #default 0.03# 
peakParam$ampThr <- 0.3 # amplitude value to threshold small peaks # 
peakParam$minPeakWidth <- 0.005 #min peak width in ppm scale
peakParam$iFrameLen<-11 #Savitzky-Golay frame length in ppm scale
peakParam$iOrder<-3 #polynomial order of Savitzky - Golay filter
peakParam$peakEdgeMax<-0.2 

#segmentate a test spectrum (10th sample)

Spectr<-Sp[10,]
testSegments<- segmentateSp(Spectr, peakParam) 

mQTL documentation built on May 1, 2019, 7:30 p.m.