mQTL.NMR (version 1.6.0)

align_mQTL: 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

datafile

The main input file of raw spectra in the csvs format

outdat

The output file of aligned spectra in the csvs format

idx

index of reference spectrum

Value

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

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.

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)