process_mQTL {mQTL.NMR} | R Documentation |
Function to process the tissue extract of the individuals for QTL analysis
process_mQTL(datfile, genfile, nperm = 0)
datfile |
a text file with phenotype data |
genfile |
a text file with genotype data |
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.
# 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)