normalise_mQTL: Normalisation of metabolomic data

In lhedjazi/mQTL.NMR: Metabolomic Quantitative Trait Locus Mapping for 1H NMR data

Description

Takes use of the base function normalise to provide a normalised metabolomic data file.

Usage

normalise_mQTL(infile,outfile,method,refIdx=1, noiseInt=c(11,12))

Arguments

infile	a text file with non-normalised spectra profiles
outfile	a text file with normalised spectra profiles
method	a character defining the normalization method: - Constant sum normalisation (method<-'CS') - Constant noise normalisation (method<-'CN') - Qoutient probabilistic method (method<-'PQN') - Linear baseline normalisation (method<-'LBN') - Auto-scaling (method<-'AS') - Pareto scaling (method<-'PS')
refIdx	index of reference individual (set by the user)
noiseInt	noise region on the resonance axis as an interval (ex. [11,12] ppm)

Value

a file containing normalised spectra profiles

Author(s)

Lyamine Hedjazi

See Also

normalise

Examples

# Download data files
load_datafiles()

# Format data

format_mQTL(phenofile,genofile,physiodat,cleandat,cleangen)

# Constant Sum normlisation
nmeth<-'CS'
normalise_mQTL(cleandat,CSnorm,nmeth)

lhedjazi/mQTL.NMR documentation built on May 31, 2019, 10:47 p.m.