attachSegments: Concatenation of test and reference segments

In mQTL: Metabolomic Quantitative Trait Locus Mapping

Description

Concatenation of test and reference segments to ensure one-to-one correspondence.

Usage

attachSegments(refSegments,testSegments)

Arguments

refSegments	segments of the reference spectrum
testSegments	segments of the test spectrum

Details

The algorithm:

1. For each reference segment within segment boundaries, i.e. between initial and final positions, find all centre (middle) positions of test segments and merge those segments, if more than one centre position is found

2. Apply the same procedure for each test segment

Value

A list:

segments$start	start of each concatenated test segment
segments$PeakLeftBoundary	peak left boundary of each concatenated test segment
segments$PeakRightBoundary	peak right boundary of each concatenated test segment
segments$Peaks	peaks of each concatenated test segment
segments$end	end of each concatenated test segment
segments$end	center of each concatenated test segment

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

matchSegments

Examples

## Not run: 

## Data

Sp=matrix(rnorm(10*13454,mean=0,sd=1), nrow=10,ncol=13454)

##Segmentation parameters

peakParam=list()
peakParam$ppmDist <- 0.03# (ppm)  # distance to concatenate adjacent peaks #default 0.03# 
peakParam$ampThr <- 0.3 # amplitude value to threshold small peaks # 
peakParam$minPeakWidth <- 0.005 #min peak width in ppm scale
peakParam$iFrameLen<-11 #Savitzky-Golay frame length in ppm scale
peakParam$iOrder<-3 #polynomial order of Savitzky - Golay filter
peakParam$peakEdgeMax<-0.2 

##Reference spectrum selection

step<-0.02 # Recursion step (default 0.02)
index<-selectRefSp(Sp,step)
refSp<-Sp[index,]

#segmentate a reference spectrum

refSegments<- segmentateSp(refSp, peakParam) # segmentate reference spectrum

#segmentate a test spectrum

spectrum<-Sp[10,]
testSegments<- segmentateSp(spectrum, peakParam) # segmentate test spectrum (10th sample)

# match test and reference segments

attachedSegs<-attachSegments(refSegments,testSegments)


## End(Not run)

mQTL documentation built on May 1, 2019, 7:30 p.m.