pre_mQTL {mQTL.NMR} | R Documentation

## Statistical Recoupling of variables for mQTL analysis

### Description

Makes use of SRV to preprocess metabolomic data for dimensionality reduction by statistical recoupling of variables

### Usage

    pre_mQTL(infile, outfile, RedMet="SRV", met="sum", corrT = 0.9, BinWidth=0.01)

### Arguments

`infile` | metabolomic datafile in csvs format
`outfile` | reduced metabolomic datafile in csvs format
`met` | a charcater specifying the used statistical summary
`RedMet` | a charcater indicating the used dimensionality reduction method: Redmet="SRV" for statistical recoupling of variables and Redmet="bin" to apply the bining approach
`corrT` | a numerical parameter indicating correlation threshold
`BinWidth` | a numerical parameter indicating the bining width

### Details

mQTL-NMR package implements two dimensionality reduction methods. The first one concerns the SRV algorithm which forms clusters of variables using a measure of a local spectral dependency. The second one concerns the classical bining method which divides the spectra into evenly spaced windows (bins) whose width commonly ranges between 0.001 and 0.05 ppm.

### Value

variables are associated into a series of clusters (or bins). This function provides in output the paramaters of the clusters (min and max borders, mean,...)

### Author(s)

Lyamine Hedjazi

### References

- Blaise,B. et al (2009) Statistical recoupling prior to significance testing in nuclear magnetic resonance based metabonomics, Anal. Chem., 81(15), 6242-6251. - S praul, M.; Neidig, P.; Klauck, U.; Kessler, P.; Holmes, E.; Nicholson, J. K.; Sweatman, B.C.; Salman, S.R.; Farrant, R.D.; Rahr, E.; et al. J.Pharm. Biomed. Anal. 1994, 12, 1215-1225.

### See Also

`SRV`,`post_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)

    # Dimensionality reduction
    met="rectangle" # choose the statistical summarizing measure ("max","sum","trapez",...)
    RedMet="SRV" # reduction method ("SRV" or "bin")

    pre_mQTL(aligdat, reducedF, RedMet="SRV",met, corrT=0.9)

[Package mQTL.NMR version 1.14.0 Index]