alignSp: Base function for Spectrum Alignment

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

Description

Alignment of spectrum segement to the spectrum of interest

Usage

alignSp(refSp, refSegments, intSp, intSegments, recursion, MAX_DIST_FACTOR, MIN_RC)

Arguments

refSp	a vector specifying the reference spectrum
refSegments	a list characterizing the reference segments (start, end, peaks, ...)
intSp	a vector specifiying the spectrum of intrest
intSegments	a list characterizing the segment of interest (start, end, peaks, ...)
recursion	A list defining defaut values of the parameters of recursive alignment(minimal segment width, recursion step, resamblance, acceptance, ...)
MAX_DIST_FACTOR	distance matching parameter (0.5*peak width)
MIN_RC	minimum resamblance coefficient

Value

alignedSpectrum

aligned spectrum as a vector

Author(s)

Lyamine Hedjazi

See Also

align_mQTL

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 a test spectrum
testSegments<- segmentateSp(Sp[1,], peakParam) 

##attach test and reference segments
attachedSegs<-attachSegments(refSegments,testSegments)

##Match test and reference segments
attach(attachedSegs)
Segs<-matchSegments(refSp,Sp[1,],testSegmentsNew,refSegmentsNew,MAX_DIST_FACTOR, MIN_RC)

##Align test spectrum
attach(Segs)
SpAlg<- alignSp(refSp,refSegs,Sp[1,],testSegs,recursion,MAX_DIST_FACTOR,MIN_RC)

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