R/PeakML.Isotope.getFCMtxAbun.R

In andzajan/mzmatch.R: mzmatch and PeakML integration for XCMS.

PeakML.Isotope.getFCMtxAbun <- function (trendList, sampleGroups, followCarbon, element){

	numCarbons <-  length(trendList[[1]])
	plotMtx <- matrix(nrow = 3, ncol = length(sampleGroups))
	dimnames(plotMtx) <- list(c("bottom", "top1", "top2"), sampleGroups)
	#colVector <- plotMtx

	N <- numCarbons
	M <- followCarbon - 1
	P <- 0.0112 # natural abundance of Carbon 1.12%
	if (element=="N") P <- 0.00368

	NatAbuC <- choose(N,M)*(P)^M*((1-P)^(N-M))

	for (sam in 1:length(sampleGroups)){
		for (row in 1:length(rownames(plotMtx))){			# This is to plot the natural abundance

			x <- trendList[[sam]][[followCarbon]]
			y <- trendList[[sam]][[1]]

			if (is.null(x)){
				x <- 0
			}
			if (is.null(y)){
				y <- 0
			}

			z <- y * NatAbuC

			bottom <- min(x,z)
			top <- max(x,z) - min(x,z)

			VAL <- 0.000
			if (row == 1){
				VAL <- bottom
			} else if(row == 2){
				if ((x-z)<=0){
					VAL <- top
				}
			} else if(row ==3){
				if ((x-z)>=0){
					VAL <- top
				}
			}

			plotMtx[row, sam] <- VAL
		}
	}
	plotMtx
}