process_mGWA: Metabolomic Genome-Wide Association analysis for a set of...
In lhedjazi/mQTL.NMR: Metabolomic Quantitative Trait Locus Mapping for 1H NMR data

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

Test for association between a trait and genetic polymorphism

1	process_mGWA(phenofile = phenofile, genofile = genofile, nperm = 0, gtmodel = "overdominant", covarList = c("sex", "age"))

`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")

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.

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

Lyamine Hedjazi

Aulchenko, Y.S.; Ripke, S.; Isaacs, A.; van Duijn, C.M. Bioinformatics 2007, 23, 1294-1296.

format_mGWA

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")