alignSp {mQTL.NMR} | R Documentation

## Base function for Spectrum Alignment

### 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)

[Package mQTL.NMR version 1.14.0 Index]