mQTL: Metabolomic Quantitative Trait Locus Mapping
Version 1.0

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.

AuthorLyamine Hedjazi and Jean-Baptiste Cazier
Date of publication2013-10-21 12:44:23
MaintainerLyamine Hedjazi <l.hedjazi@fondation-ican.com>
LicenseGPL
Version1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("mQTL")

Getting started

Package overview

Popular man pages

format_mQTL: Routine to reformat the data into the required format
matchSegments: Matching of the segment of interest to the corresponding...
mQTL-package: Metabolomic Quantitative Trait Locus mapping
normalise: Normalisation of metabolomic data
ppersp: Plot a 3-D profile of LODs
sgolay: Find the matrix of differentiation filters
SRV: Statistical Recoupling of Variables
See all...

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...
mQTL-package: Metabolomic Quantitative Trait Locus mapping
normalise: Normalisation of metabolomic data
peakPeaks: Peak picking algorithm
post_mQTL: Plot top LOD results
ppersp: Plot a 3-D 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
mQTL-package 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/mQTL-package.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
mQTL documentation built on May 19, 2017, 7:28 a.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.