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mQTL.NMR (version 1.6.0)

Metabolomic Quantitative Trait Locus Mapping for 1H NMR data

Description

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.

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Version

Version

1.6.0

License

Artistic-2.0

Maintainer

Lyamine Hedjazi

Last Published

February 15th, 2017

Functions in mQTL.NMR (1.6.0)

Circular genome-metabolome plot for mQTL.NMR

Base function of normalisation

Statistical Recoupling of variables for mQTL analysis

Automated selection of a reference spectrum

Segmentation of a spectrum of interest

Plot SRV clusters

Routine to reformat the data of animal crosses into the required format to perform mQTL mapping

Plot a color scale layer

Plot NMR profile plus SRV regions

setup of alignment parameters

Normalisation of metabolomic data

Matching the segment of interest to the corresponding reference

Routine to reformat the data into the required format to perform mGWAS

Statistical Recoupling of Variables

Function to summarize the mQTL mapping results of all the runs and their differences

Find the matrix of differentiation filters

Calculate smoothed derivates

Plot a 3-D profile of LODs

Concatenation of test and reference segments

mQTL.NMR-package

Metabolomic Quantitative Trait Locus mapping for 1H NMR data

Peak picking algorithm

Plot top lod SRV clusters

Base function for Spectrum Alignment

Load demo data files

Load data files for examples

Peak alignment and normalisation of metabolomic data

Plot top SRV clusters

segmentaion and recursive alignment parameters

Plot top LOD results

Metabolomic Genome-Wide Association analysis for a set of independent individuals