mQTL.NMR (version 1.6.0)

process_mGWA: 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")

Value

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

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.

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")