mQTL.NMR: Metabolomic Quantitative Trait Locus Mapping for 1H NMR data
Version 1.10.0

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.

AuthorLyamine Hedjazi and Jean-Baptiste Cazier
Bioconductor views Cheminformatics Genetics Metabolomics SNP
Date of publicationNone
MaintainerLyamine Hedjazi <mqtl@ican-institute.org>
LicenseArtistic-2.0
Version1.10.0
URL http://www.ican-institute.org/tools/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("mQTL.NMR")

Getting started

Package overview

Popular man pages

align_mQTL: Peak alignment and normalisation of metabolomic data
alignSp: Base function for Spectrum Alignment
circle_mQTL: Circular genome-metabolome plot for mQTL.NMR
mQTL.NMR-package: Metabolomic Quantitative Trait Locus mapping for 1H NMR data
post_mQTL: Plot top LOD results
segmentateSp: Segmentation of a spectrum of interest
SRV.plot: Plot SRV clusters
See all...

All man pages Function index File listing

Man pages

align_mQTL: Peak alignment and normalisation of metabolomic data
alignSp: Base function for Spectrum Alignment
attachSegments: Concatenation of test and reference segments
circle_mQTL: Circular genome-metabolome plot for mQTL.NMR
configureRSPA: segmentaion and recursive alignment parameters
format_mGWA: Routine to reformat the data into the required format to...
format_mQTL: Routine to reformat the data of animal crosses into the...
load_datafiles: Load data files for examples
load_demo_data: Load demo data files
matchSegments: Matching the segment of interest to the corresponding...
mQTL.NMR-package: Metabolomic Quantitative Trait Locus mapping for 1H NMR data
normalise: Base function of normalisation
normalise_mQTL: 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_mGWA: Metabolomic Genome-Wide Association analysis for a set of...
process_mQTL: mQTL mapping
segmentateSp: Segmentation of a spectrum of interest
selectRefSp: Automated selection of a reference spectrum
setupRSPA: setup of alignment parameters
sgolay: Find the matrix of differentiation filters
sgolayDeriv: Calculate smoothed derivates
simple.plot: Plot NMR profile plus SRV regions
SRV: Statistical Recoupling of Variables
SRV_lod.plot: Plot top lod SRV clusters
SRV.plot: Plot SRV clusters
summary_mQTL: Function to summarize the mQTL mapping results of all the...
Top_SRV.plot: Plot top SRV clusters

Functions

Centered Source code
FFTcorr Source code
NMR.plot Source code
Plot_summary Source code
SRV Man page Source code
SRV.plot Man page Source code
SRV_lod.plot Man page Source code
Top_SRV.plot 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
circle_mQTL Man page Source code
circlelocations Source code
comparePeaks Source code
configureRSPA Man page Source code
corrcoef_aligned Source code
diff_res Source code
drawcirculargenome Source code
drawspline Source code
drawstraightmetabolome Source code
drop_outliers Source code
findMid Source code
format_mGWA Man page Source code
format_mQTL Man page Source code
getAmpThr Source code
getCorellation Source code
get_central_pos Source code
getchromosomelength Source code
getgenomelength Source code
load_datafiles Man page Source code
load_demo_data Man page Source code
localRecurAlign Source code
locationtoaxis Source code
locationtocircle Source code
mQTL.NMR Man page
mQTL.NMR-package Man page
matchSegments Man page Source code
msea Source code
normalise Man page Source code
normalise_mQTL 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_mGWA 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 Man page Source code
sgolay Man page Source code
sgolayDeriv Man page Source code
shift Source code
simple.plot Man page 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

DESCRIPTION
NAMESPACE
R
R/Centered.R
R/FFTcorr.R
R/NMR.plot.R
R/Plot_summary.R
R/SRV.R
R/SRV.plot.R
R/SRV_lod.plot.R
R/Top_SRV.plot.R
R/UVscaled.R
R/add_peak.R
R/alignSp.R
R/align_mQTL.R
R/arrow.plot.R
R/attachSegments.R
R/circle_mQTL.R
R/circlelocations.R
R/comparePeaks.R
R/configureRSPA.R
R/corrcoef_aligned.R
R/diff_res.R
R/drawcirculargenome.R
R/drawspline.R
R/drawstraightmetabolome.R
R/drop_outliers.R
R/findMid.R
R/format_mGWA.R
R/format_mQTL.R
R/getAmpThr.R
R/getCorellation.R
R/get_central_pos.R
R/getchromosomelength.R
R/getgenomelength.R
R/load_datafiles.R
R/load_demo_data.R
R/localRecurAlign.R
R/locationtoaxis.R
R/locationtocircle.R
R/matchSegments.R
R/msea.R
R/normalise.R
R/normalise_mQTL.R
R/panel.cor.R
R/panel.hist.R
R/peakPeaks.R
R/pinv.R
R/post_mQTL.R
R/ppersp.R
R/pplot.R
R/ppmToPt.R
R/pre_mQTL.R
R/process_mGWA.R
R/process_mQTL.R
R/psave.R
R/read.cross.gary.R
R/rectangle.R
R/recurAlign.R
R/run_QTL.R
R/running.R
R/segmentate.R
R/segmentateSp.R
R/selectRefSp.R
R/set_baseline.R
R/setupRSPA.R
R/sgolay.R
R/sgolayDeriv.R
R/shift.R
R/simple.plot.R
R/summarize.R
R/summary_mQTL.R
R/trapeze.R
R/unite_segments.R
R/validatePeaks.R
R/validateSegments.R
R/zeroPad.R
build
build/vignette.rds
inst
inst/CITATION.Rd
inst/doc
inst/doc/FAQ.R
inst/doc/FAQ.Rnw
inst/doc/FAQ.pdf
inst/doc/mQTLUse.R
inst/doc/mQTLUse.Rnw
inst/doc/mQTLUse.pdf
inst/extdata
inst/extdata/covarFile.txt
inst/extdata/genofile.txt
inst/extdata/hreducedF.txt
inst/extdata/human.geno.ped
inst/extdata/human.pheno.txt
inst/extdata/humanMap.map
inst/extdata/phenofile.txt
inst/extdata/physiodat.txt
inst/extdata/rectangle_SRV.ppm
inst/extdata/reducedF.txt
inst/extdata/results.rda
man
man/SRV.Rd
man/SRV.plot.Rd
man/SRV_lod.plot.Rd
man/Top_SRV.plot.Rd
man/alignSp.Rd
man/align_mQTL.Rd
man/attachSegments.Rd
man/circle_mQTL.Rd
man/configureRSPA.Rd
man/format_mGWA.Rd
man/format_mQTL.Rd
man/load_datafiles.Rd
man/load_demo_data.Rd
man/mQTL.NMR-package.Rd
man/matchSegments.Rd
man/normalise.Rd
man/normalise_mQTL.Rd
man/peakPeaks.Rd
man/post_mQTL.Rd
man/ppersp.Rd
man/pplot.Rd
man/pre_mQTL.Rd
man/process_mGWA.Rd
man/process_mQTL.Rd
man/segmentateSp.Rd
man/selectRefSp.Rd
man/setupRSPA.Rd
man/sgolay.Rd
man/sgolayDeriv.Rd
man/simple.plot.Rd
man/summary_mQTL.Rd
vignettes
vignettes/CSVSFilesFormat.png
vignettes/FAQ.Rnw
vignettes/FilesFormat.png
vignettes/mQTLUse.Rnw
mQTL.NMR documentation built on May 20, 2017, 9:19 p.m.

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