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

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.

Author
Lyamine Hedjazi and Jean-Baptiste Cazier
Date of publication
None
Maintainer
Lyamine Hedjazi <mqtl@ican-institute.org>
License
Artistic-2.0
Version
1.8.0
URLs

View on Bioconductor

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

Files in this package

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