mQTL provides a complete QTL analysis pipeline for metabolomic data. Distinctive features include normalisation using PQN approach, peak alignment using RSPA approach, dimensionality reduction using SRV approach and finally QTL mapping using R/qtl package.
Author  Lyamine Hedjazi and JeanBaptiste Cazier 
Date of publication  20131021 12:44:23 
Maintainer  Lyamine Hedjazi <l.hedjazi@fondationican.com> 
License  GPL 
Version  1.0 
Package repository  View on CRAN 
Installation  Install the latest version of this package by entering the following in R:



All man pages Function index File listing
Man pages  

align_mQTL: Peak alignement and normalisation of metabolomic data  
alignSp: Base function for Spectrum Alignment  
attachSegments: Concatenation of test and reference segments  
format_mQTL: Routine to reformat the data into the required format  
matchSegments: Matching of the segment of interest to the corresponding...  
mQTLpackage: Metabolomic Quantitative Trait Locus mapping  
normalise: Normalisation of metabolomic data  
peakPeaks: Peak picking algorithm  
post_mQTL: Plot top LOD results  
ppersp: Plot a 3D profile of LODs  
pplot: Plot a color scale layer  
pre_mQTL: Statistical Recoupling of variables for mQTL analysis  
process_mQTL: mQTL mapping  
segmentateSp: Segmentation of a spectrum of interest  
selectRefSp: Automated selection of a reference spectrum  
sgolay: Find the matrix of differentiation filters  
sgolayDeriv: Calculate smoothed derivates  
SRV: Statistical Recoupling of Variables  
SRV_Corr: Statistical recoupling of variables in a supervised context  
summary_mQTL: Function to summarize the results of a all the runs and their... 
Functions  

Centered  Source code 
FFTcorr  Source code 
NMR.plot  Source code 
Plot_summary  Source code 
SRV  Man page Source code 
SRV.plot  Source code 
SRV_Corr  Man page Source code 
UVscaled  Source code 
add_peak  Source code 
alignSp  Man page Source code 
align_mQTL  Man page Source code 
arrow.plot  Source code 
attachSegments  Man page Source code 
comparePeaks  Source code 
configureRSPA  Source code 
corrcoef_aligned  Source code 
diff_res  Source code 
drop_outliers  Source code 
findMid  Source code 
format_mQTL  Man page Source code 
getAmpThr  Source code 
getCorellation  Source code 
get_central_pos  Source code 
localRecurAlign  Source code 
mQTL  Man page 
mQTLpackage  Man page 
matchSegments  Man page Source code 
msea  Source code 
normalise  Man page Source code 
panel.cor  Source code 
panel.hist  Source code 
peakPeaks  Man page Source code 
pinv  Source code 
post_mQTL  Man page Source code 
ppersp  Man page Source code 
pplot  Man page Source code 
ppmToPt  Source code 
pre_mQTL  Man page Source code 
process_mQTL  Man page Source code 
psave  Source code 
read.cross.gary  Source code 
rectangle  Source code 
recurAlign  Source code 
run_QTL  Source code 
running  Source code 
segmentate  Source code 
segmentateSp  Man page Source code 
selectRefSp  Man page Source code 
set_baseline  Source code 
setupRSPA  Source code 
sgolay  Man page Source code 
sgolayDeriv  Man page Source code 
shift  Source code 
simple.plot  Source code 
summarize  Source code 
summary_mQTL  Man page Source code 
trapeze  Source code 
unite_segments  Source code 
validatePeaks  Source code 
validateSegments  Source code 
zeroPad  Source code 
Files  

NAMESPACE
 
R
 
R/mQTL.R  
MD5
 
DESCRIPTION
 
man
 
man/pre_mQTL.Rd  
man/alignSp.Rd  
man/mQTLpackage.Rd  
man/pplot.Rd  
man/segmentateSp.Rd  
man/summary_mQTL.Rd  
man/matchSegments.Rd  
man/process_mQTL.Rd  
man/ppersp.Rd  
man/post_mQTL.Rd  
man/SRV_Corr.Rd  
man/normalise.Rd  
man/sgolay.Rd  
man/sgolayDeriv.Rd  
man/format_mQTL.Rd  
man/selectRefSp.Rd  
man/align_mQTL.Rd  
man/attachSegments.Rd  
man/SRV.Rd  
man/peakPeaks.Rd 
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