mQTL.NMR (version 1.6.0)

format_mGWA: Routine to reformat the data into the required format to perform mGWAS

Description

This function enables to reformat data into the proper format. The user should provides in input metabolomic file, Genotype file, map file and a file containing sex, age and individual IDs.

Usage

format_mGWA(datafile, genofile1, genofile2, covarfile, outdat, outgeno)

Arguments

datafile

metabolomic data file

genofile1

genotype file in the "ped" format

genofile2

map file containing more information on SNP marker (position, ...)

covarfile

a text file contains covariates such as age or sex

outdat

output data file with formatted phenotype data in csvs format

outgeno

output data file with formatted genotype data in csvs format

Value

formatted phenotype and genotype data files (in format csvs) are written to the user working directory (it is therefore preferable that the user create a new directory to be used throughout the study)

See Also

format_mQTL, process_mGWA

Examples

load_datafiles()
format_mGWA(human.pheno, human.geno, humanMap, covarFile,cleandat, cleangen)