# Metabolomic Quantitative Trait Locus Mapping for 1H NMR data

## Documentation for package ‘mQTL.NMR’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

mQTL.NMR-package | Metabolomic Quantitative Trait Locus mapping for 1H NMR data
alignSp | Base function for Spectrum Alignment
align_mQTL | Peak alignment and normalisation of metabolomic data
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 perform mGWAS
format_mQTL | Routine to reformat the data of animal crosses into the required format to perform mQTL mapping
load_datafiles | Load data files for examples
load_demo_data | Load demo data files
matchSegments | Matching the segment of interest to the corresponding reference
mQTL.NMR | 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 independent individuals
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.plot | Plot SRV clusters
SRV_lod.plot | Plot top lod SRV clusters
summary_mQTL | Function to summarize the mQTL mapping results of all the runs and their differences
Top_SRV.plot | Plot top SRV clusters