mQTL.NMR-package {mQTL.NMR} | R Documentation |
mQTL.NMR provides a complete mQTL analysis pipeline for 1H NMR data. Distinctive features include normalisation using most-used approaches, peak alignment using RSPA approach, dimensionality reduction using SRV and binning approaches, and mQTL analysis for animal and human cohorts.
Package: | mQTL.NMR |
Type: | Package |
Version: | 0.99.2 |
Link: | http://www.ican-institute.org/tools |
Date: | 2014-05-19 |
License: | Artistic-2.0 |
Main fucntions:
format_mQTL
: generates the proper format of animal crosses data
format_mGWA
: generates the proper format of human data
align_mQTL
: peak alignment
normalise_mQTL
: normalisation of metabolomic data using different approaches (Probabilistic quotient, constant sum,...)
pre_mQTL
: dimension reduction by statistical recoupling of variables or bining
process_mQTL
: computes LODs using extended Haley-Knott method for animal crosses
process_mGWA
: computes p-values using a standard linear regression approach for human
post_mQTL
: plots the results of a given run
summary_mQTL
: provides the results as a table
simple.plot
: Plots a region of NMR profile
SRV.plot
: Plots the regions identified by SRV in NMR profiles
ppersp
: Plot 3-D profile of LODs as function of genomic position and chemical shift
pplot
: Plot a color scale layer
Top_SRV.plot
: Plot top SRV clusters for structural assignment
circle_mQTL
: Plot a circular genome-metabolome plot
Lyamine Hedjazi and Jean-Baptiste Cazier
Maintainer: Lyamine Hedjazi <mqtl@ican-institute.org>
- L. HEDJAZI, D. GAUGUIER, P. ZALLOUA, J. NICHOLSON, M-E DUMAS and J-B CAZIER, mQTL-NMR: an integrated suite for genetic mapping of quantitative variations of 1H NMR-based metabolic profiles, Analytical Chemistry, 2015, doi: 10.1021/acs.analchem.5b00145.
# Download data files load_datafiles() # Format data format_mQTL(phenofile,genofile,physiodat,cleandat,cleangen) # Constant Sum normlisation nmeth<-'CS' normalise_mQTL(cleandat,CSnorm,nmeth) # Alignment align_mQTL(CSnorm,aligdat) # Dimensionality reduction met="rectangle" # choose the statistical summarizing measure ("max","sum","trapez",...) RedMet="SRV" # reduction method ("SRV" or "bin") pre_mQTL(aligdat, reducedF, RedMet="SRV",met, corrT=0.9) # mQTL mapping results<- list() # a list to stock the mQTL mapping results nperm<- 0 # number of permutations if required results<-process_mQTL(reducedF, cleangen, nperm) ## Post-Process post_mQTL(results) ## Summarize redfile<-"rectangle_SRV.ppm" summary_mQTL(results,redfile,T=8) #plot circular genome circle_mQTL(results, Th=8,spacing=0) ## visualisation and metabolite identification #plot NMR profile simple.plot(file=cleandat,lo=3.02,hi=3.08,k=1:20,title="NMR profile") #plot SRV regions SRV.plot(file1=cleandat,file2=rectangle_SRV,lo=3.02,hi=3.08,k=1:20,title="Cluster plot") #plot lod for the region of interest SRV_lod.plot(results,rectangle_SRV,Th=1) #plot top lod SRV regions Top_SRV.plot(file1=cleandat,file2=rectangle_SRV,results=results,met=met,intMeth="mean")