R: Base function for Spectrum Alignment

alignSp {mQTL} | R Documentation

## Base function for Spectrum Alignment

### Description

Alignement of spectrum segement to a spectrum of interest

### Usage

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

### Arguments

`refSp` | reference spectrum
`refSegments` | refrence segments
`intSp` | spectrum of intrest
`intSegments` | segments of intrest
`recursion` | parameters for recursive alignment
`MAX_DIST_FACTOR` | the distance matching parameter (0.5*peak width)
`MIN_RC` | minimum resamblance coefficient

### Value

`alignedSpectrum` | aligned spectrum
`extendedSegments` | extended segments

### Author(s)

Lyamine Hedjazi

Maintainer: Lyamine Hedjazi <l.hedjazi@fondation-ican.com>

### See Also

`align_mQTL`

### Examples

    ## 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 # maximal peak edge

    ##Recusrsion alignment parameters

    recursion=list()
    recursion$resamblance<-0.95# Stop criterium of the recursion indicating
    #the complete alignment of segment peaks
    recursion$segShift<-0.02#(ppm)  max peak shift for large peaks
    recursion$inbetweenShift<-0.02 #(ppm) max shift for small peaks
    recursion$acceptance<-0.5 # if resemblance after the alignment between modified test
    recursion$minSegWidth<-0.01 #(ppm) Stop criteria of the recursion - the size of the smallest peak
    recursion$step<-0.02 # Recursion step (default 0.02)

    ## Normalisation

    normD<-normalise(Sp,'prob')

    ## Reference spectrum selection

    index<-selectRefSp(normD$Sp,recursion$step)
    refSp<-normD$Sp[index,] # reference spectrum picked-up

    ##segmentate a reference spectrum

    refSegments<- segmentateSp(refSp, peakParam) # segmentate reference spectrum

    ##segmentate a test spectrum

    spectrum<-normD$Sp[10,]
    testSegments<- segmentateSp(spectrum, peakParam) # segmentate test spectrum (10th sample)

    #match test and reference segments

    attachedSegs<-attachSegments(refSegments,testSegments)

    refSegments<-attachedSegs$refSegmentsNew
    testSegments<-attachedSegs$testSegmentsNew

    ##matching parameters

    MAX_DIST_FACTOR<-0.5 # The distance matching parameter (0.5*peak_width)
    MIN_RC<-0.25 # Minimum resamblance coefficient

    Segs<-matchSegments(refSp,spectrum, testSegments,refSegments,MAX_DIST_FACTOR,MIN_RC)

    #align a test spectrum

    refSgs<-Segs$refSegs
    tstSgs<-Segs$testSegs

    SpAlg<- alignSp(refSp,refSgs,spectrum,tstSgs,recursion,MAX_DIST_FACTOR,MIN_RC)

    ## End(Not run)

[Package mQTL version 1.0 Index]