R/setupRSPA.R

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

setupRSPA <-
function(ppm){

# setup of alignment parameters
# input: ppm - chemical shift scale
# L. Hedjazi, ICAN, 2013


MAX_DIST_FACTOR<-numeric()
MIN_RC<-numeric()

# Configuration of the algorithm invariant parameters 

configureRSPA(ppm)

### These parameters can be changed to improve the algorithm performance
#################### Recursive alignment parameters ########################

recursion$resamblance<-0.95 # Stop criterium of the recursion indicating
#the complete alignment of segment peaks
# default 98#

######################## Segmentation parameters############################
peakParam$ppmDist <- 0.03# (ppm)  #distance to concatenate adjacent peaks 
#to represent a multiplet in a single segment ### default 0.03# 
peakParam$ampThr <- 0.3 # amplitude value to threshold small peaks # 
#[] - automatic determination based on the 5# of the most intensive peaks

############Prevention of Misalignment on a local scale##############
recursion$segShift<-0.02#(ppm)  max peak shift for large peaks
recursion$inbetweenShift<-0.02 #(ppm) max shift for small peaks
recursion$acceptance<-0.5 # if resemblance after the alignment between modified test 
#and reference segments is less than the acceptance value, the alignment is not accepted. 
#Higher value is more stringent, and align only highly resemble peaks.

if (!missing(ppm)){
    peakParam$ppmDist<-ppmToPt(peakParam$ppmDist,0,ppm[2]-ppm[1])
    recursion$segShift<-ppmToPt(recursion$segShift,0,ppm[2]-ppm[1])
    recursion$inbetweenShift<-ppmToPt(recursion$inbetweenShift,0,ppm[2]-ppm[1])}

assign("peakParam", peakParam,envir = parent.frame())
assign("recursion", recursion,envir = parent.frame())
assign("MAX_DIST_FACTOR", MAX_DIST_FACTOR,envir = parent.frame())
assign("MIN_RC", MIN_RC,envir = parent.frame())
}