attachSegments {mQTL.NMR} | R Documentation

## Concatenation of test and reference segments

### Description

Concatenation of test and reference segments to ensure one-to-one correspondence.

### Usage

    attachSegments(refSegments,testSegments)

### Arguments

`refSegments` | a list characterizing the segments of the reference spectrum (start, end, peaks, center)
`testSegments` | a list characterizing the segments of the test spectrum (start,end, peaks, center)

### Details

The algorithm:

1. For each reference segment within segment boundaries, i.e. between initial and final positions, find all centre (middle) positions of test segments and merge those segments, if more than one centre position is found

2. Apply the same procedure for each test segment

### Value

A list:

`segments$start` | a vector specifiying the starting of each concatenated test segment
`segments$PeakLeftBoundary` | a list defining the peak left boundary of each concatenated test segment
`segments$PeakRightBoundary` | a list defining the peak right boundary of each concatenated test segment
`segments$Peaks` | a list specifiying the peaks information of each concatenated test segment (max position, start position, end position,...)
`segments$end` | a vector specifiying the end of each concatenated test segment
`segments$end` | a vector specifiying the center of each concatenated test segment

### 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

`matchSegments`

### 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 reference spectrum

    ##segmentate a test spectrum
    testSegments<- segmentateSp(Sp[1,], peakParam) # segmentate test spectrum (1st sample)

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

[Package mQTL.NMR version 1.14.0 Index]