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.

AuthorLyamine Hedjazi and Jean-Baptiste Cazier
Date of publicationNone
MaintainerLyamine Hedjazi <mqtl@ican-institute.org>
LicenseArtistic-2.0
Version1.8.0
http://www.ican-institute.org/tools/

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

Functions

align_mQTL Man page
alignSp Man page
attachSegments Man page
circle_mQTL Man page
configureRSPA Man page
format_mGWA Man page
format_mQTL Man page
load_datafiles Man page
load_demo_data Man page
matchSegments Man page
mQTL.NMR Man page
mQTL.NMR-package Man page
normalise Man page
normalise_mQTL Man page
peakPeaks Man page
post_mQTL Man page
ppersp Man page
pplot Man page
pre_mQTL Man page
process_mGWA Man page
process_mQTL Man page
segmentateSp Man page
selectRefSp Man page
setupRSPA Man page
sgolay Man page
sgolayDeriv Man page
simple.plot Man page
SRV Man page
SRV_lod.plot Man page
SRV.plot Man page
summary_mQTL Man page
Top_SRV.plot Man page

Files

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

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