Peak alignment and normalisation of metabolomic data

Description

Recursive Segment-Wise Peak Alignment (RSPA) for accounting peak position variation across metabolomic data

Usage

align_mQTL(datafile, outdat,idx)

Arguments

Details

The algorithm is based on the following workflow:

1. Automatic selection of a reference spectrum (if required).

2. Segmentate a reference spectrum.

3. Then for each test spectrum:

   • segmentate a test spectrum.

   • match test and reference segments.

   • align a test spectrum.

Value

It returns a file with aligned data in the csvs format.

Author(s)

Lyamine Hedjazi

References

Veselkov,K. et al (2009) Recursive Segment-Wise Peak Alignment of Biological 1H NMR Spectra for Improved Metabolic Biomarker Recovery, Anal. Chem., 81(1), 56-66.

See Also

alignSp, attachSegments, matchSegments, segmentateSp,format_mQTL, format_mQTL

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)


# Alignment
align_mQTL(CSnorm,aligdat)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(mQTL.NMR)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mQTL.NMR/align_mQTL.Rd_%03d_medium.png", width=480, height=480)
> ### Name: align_mQTL
> ### Title: Peak alignment and normalisation of metabolomic data
> ### Aliases: align_mQTL
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> # Download data files
> 
> load_datafiles()
> 
> # Format data
> 
> format_mQTL(phenofile,genofile,physiodat,cleandat,cleangen)
[1] "Start formatting the datafile /home/ddbj/local/lib64/R/library/mQTL.NMR/extdata/phenofile.txt and the genotype file /home/ddbj/local/lib64/R/library/mQTL.NMR/extdata/genofile.txt into the csvs files: met.clean.txt gen.clean.txt"
> 
> # Constant Sum normlisation
> nmeth<-'CS'
> normalise_mQTL(cleandat,CSnorm,nmeth)
[1] "Start constant sum normalisation:"
> 
> 
> # Alignment
> align_mQTL(CSnorm,aligdat)
[1] "...Automatic selection of a reference spectrum..."
Error in if ((dpDerivs[i] >= 0) && (dpDerivs[i + 1] < 0)) { : 
  missing value where TRUE/FALSE needed
Calls: align_mQTL -> segmentateSp -> peakPeaks
In addition: There were 40 warnings (use warnings() to see them)
Execution halted