process_mGWA {mQTL.NMR} | R Documentation

## Metabolomic Genome-Wide Association analysis for a set of independent individuals

### Description

Test for association between a trait and genetic polymorphism

### Usage

    process_mGWA(phenofile = phenofile, genofile = genofile, nperm = 0, gtmodel = "overdominant", covarList = c("sex", "age"))

### Arguments

`phenofile` | a text file with phenotype data
`genofile` | a text file with genotype data
`nperm` | number of permutations
`gtmodel` | genetic model ("additive","recessive","dominant","overdominant")
`covarList` | covariate variables ("sex" and/or "age")

### Details

This function makes use of metabolomic and genotype data to perform genome-wide association analysis using a standard regression method based on the GenABEL package.

### Value

2D score tables (-log10(p-value))

### Author(s)

Lyamine Hedjazi

### References

Aulchenko, Y.S.; Ripke, S.; Isaacs, A.; van Duijn, C.M. Bioinformatics 2007, 23, 1294-1296.

### See Also

`format_mGWA`

### Examples

    load_datafiles()
    format_mGWA(human.pheno, human.geno, humanMap, covarFile,hcleandat, hcleangen)

    # mQTL mapping
    results<- list() # a list to stock the mQTL mapping results
    nperm<- 0 # number of permutations if required

    results<-process_mGWA(phenofile=hreducedF, genofile=hcleangen,nperm=0, gtmodel="additive")

[Package mQTL.NMR version 1.14.0 Index]