Metabolomic Quantitative Trait Locus Mapping for 1H NMR data


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Documentation for package ‘mQTL.NMR’ version 1.6.0

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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