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

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

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.

Examples

Run this code

# NOT RUN {
# 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) 
# }