align_mQTL {mQTL.NMR} | R Documentation

## Peak alignment and normalisation of metabolomic data

### Description

Recursive Segment-Wise Peak Alignment (RSPA) for accounting peak position variation across metabolomic data

### Usage

    align_mQTL(datafile, outdat,idx)

### Arguments

`datafile` | The main input file of raw spectra in the csvs format
`outdat` | The output file of aligned spectra in the csvs format
`idx` | index of reference spectrum

### Details

The algorithm is based on the following workflow:

1. Automatic selection of a reference spectrum (if required).

2. Segmentate a reference spectrum.

3. Then for each test spectrum:

   - segmentate a test spectrum.

   - match test and reference segments.

   - align a test spectrum.

### Value

It returns a file with aligned data in the csvs format.

### 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

`alignSp`, `attachSegments`, `matchSegments`, `segmentateSp`,`format_mQTL`, `format_mQTL`

### Examples

    # Download data files

    load_datafiles()

    # Format data

    format_mQTL(phenofile,genofile,physiodat,cleandat,cleangen)

    # Constant Sum normlisation
    nmeth<-'CS'
    normalise_mQTL(cleandat,CSnorm,nmeth)

    # Alignment
    align_mQTL(CSnorm,aligdat)

[Package mQTL.NMR version 1.14.0 Index]