align_mQTL: Peak alignment and normalisation of metabolomic data
In lhedjazi/mQTL.NMR: Metabolomic Quantitative Trait Locus Mapping for 1H NMR data

Description Usage Arguments Details Value Author(s) References See Also Examples

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

1	align_mQTL(datafile, outdat,idx)

`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

The algorithm is based on the following workflow:

Automatic selection of a reference spectrum (if required).
Segmentate a reference spectrum.
Then for each test spectrum:
- segmentate a test spectrum.
- match test and reference segments.
- align a test spectrum.

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

Lyamine Hedjazi

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.

alignSp, attachSegments, matchSegments, segmentateSp,format_mQTL, format_mQTL

# 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)