process_mQTL: mQTL mapping
In mQTL.NMR: Metabolomic Quantitative Trait Locus Mapping for 1H NMR data

Description Usage Arguments Details Value Author(s) References See Also Examples

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

1	process_mQTL(datfile, genfile, nperm = 0)

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

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.

2D LOD score table

Jean-Baptiste Cazier and Hedjazi Lyamine

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

post_mQTL

# 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)