Routine to reformat the data of animal crosses into the required format to perform mQTL mapping

Description

This function enables to reformat data into the proper format. The user should provides in input metabolomic file, Genotype file and a file containing sex and pgm (parental grandmother).

Usage

format_mQTL(datafile, genofile, physdat, 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

align_mQTL,

Examples

# Download data files
load_datafiles()

# Format data

format_mQTL(phenofile,genofile,physiodat,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_mQTL.Rd_%03d_medium.png", width=480, height=480)
> ### Name: format_mQTL
> ### Title: Routine to reformat the data of animal crosses into the required
> ###   format to perform mQTL mapping
> ### Aliases: format_mQTL
> ### Keywords: function
> 
> ### ** Examples
> 
> 
> # Download data files
> load_datafiles()
> 
> # Format data
> 
> format_mQTL(phenofile,genofile,physiodat,cleandat,cleangen)
[1] "Start formatting the datafile /home/ddbj/local/lib64/R/library/mQTL.NMR/extdata/phenofile.txt and the genotype file /home/ddbj/local/lib64/R/library/mQTL.NMR/extdata/genofile.txt into the csvs files: met.clean.txt gen.clean.txt"
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>