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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("mQTL.NMR")
AuthorLyamine Hedjazi and Jean-Baptiste Cazier
Bioconductor views Cheminformatics Genetics Metabolomics SNP
Date of publicationNone
MaintainerLyamine Hedjazi <mqtl@ican-institute.org>
LicenseArtistic-2.0
Version1.8.0
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

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

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

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

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