process_mQTL {mQTL.NMR} | R Documentation

## mQTL mapping

### Description

Function to process the tissue extract of the individuals for QTL analysis

### Usage

    process_mQTL(datfile, genfile, nperm = 0)

### Arguments

`datfile` | a text file with phenotype data
`genfile` | a text file with genotype data
`nperm` | `nperm`

### Details

This function makes use of metabolomic and genotype data to perform QTL analysis based on the R/QTL package, for mapping quantitative trait loci. In particular, it makes use of the extended Haley-Knott method to optimize the LOD score evaluation and avoid problems with missing genotypes.

### Value

2D LOD score table

### Author(s)

Jean-Baptiste Cazier and Hedjazi Lyamine

### References

Broman,K., et al (2006) R/qtl: QTL mapping in experimental crosses, Bioinformatics, 19(7), 889-890.

### See Also

`post_mQTL`

### Examples

    # Download data files

    load_datafiles()

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

[Package mQTL.NMR version 1.14.0 Index]