mQTL.NMR (version 1.6.0)

process_mQTL: 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

Value

2D LOD score table

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.

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)