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mQTL.NMR (version 1.2.0)

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

1.2.0

License

Artistic-2.0

Maintainer

Lyamine Hedjazi

Last Published

February 15th, 2017

Functions in mQTL.NMR (1.2.0)

Concatenation of test and reference segments

Circular genome-metabolome plot for mQTL.NMR

Plot a color scale layer

Statistical Recoupling of variables for mQTL analysis

Calculate smoothed derivates

Plot NMR profile plus SRV regions

Base function for Spectrum Alignment

Peak alignment and normalisation of metabolomic data

mQTL.NMR-package

Metabolomic Quantitative Trait Locus mapping for 1H NMR data

Normalisation of metabolomic data

setup of alignment parameters

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

Load data files for examples

Plot top LOD results

Plot a 3-D profile of LODs

Plot top SRV clusters

Find the matrix of differentiation filters

Load demo data files

Matching the segment of interest to the corresponding reference

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

Statistical Recoupling of Variables

Plot top lod SRV clusters

Base function of normalisation

Peak picking algorithm

Plot SRV clusters

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

segmentaion and recursive alignment parameters

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

Segmentation of a spectrum of interest

Automated selection of a reference spectrum