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

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)

Author(s)

Lyamine Hedjazi

See Also

format_mQTL, process_mGWA

Examples

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

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(mQTL.NMR)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mQTL.NMR/format_mGWA.Rd_%03d_medium.png", width=480, height=480)
> ### Name: format_mGWA
> ### Title: Routine to reformat the data into the required format to perform
> ###   mGWAS
> ### Aliases: format_mGWA
> ### Keywords: function
> 
> ### ** Examples
> 
> load_datafiles()
> format_mGWA(human.pheno, human.geno, humanMap, covarFile,cleandat, cleangen)
[1] "Start formatting the datafile /home/ddbj/local/lib64/R/library/mQTL.NMR/extdata/human.pheno.txt and the genotype files /home/ddbj/local/lib64/R/library/mQTL.NMR/extdata/human.geno.ped /home/ddbj/local/lib64/R/library/mQTL.NMR/extdata/humanMap.map into files: met.clean.txt gen.clean.txt"
Reading map from file '/home/ddbj/local/lib64/R/library/mQTL.NMR/extdata/humanMap.map' ...
... done.  Read positions of 99 markers from file '/home/ddbj/local/lib64/R/library/mQTL.NMR/extdata/humanMap.map'
Reading genotypes from file '/home/ddbj/local/lib64/R/library/mQTL.NMR/extdata/human.geno.ped' ...
...done.  Read information for 217 people from file '/home/ddbj/local/lib64/R/library/mQTL.NMR/extdata/human.geno.ped'
Analysing marker information ...
Writing to file 'gen.clean.txt' ...
... done.
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>