R/combScans.R

In binneR: Spectral Processing for High Resolution Flow Infusion Mass Spectrometry

# Combine scan ranges and retrieve given scans
# @name combScans
# @description A function that will split a peak list into appropriate modes, retrieve peak matrices of the supplied relevant scans and combine scan ranges. 
# @param x A peak list containing peak matrices for each scan
# @param scans A vector of scan numbers that should be retrieved 
# @param sranges A list of vectors containing the scan events present 
# @param modes A vector of strings denoting mode names
# @return A list containing peak lists for the relevant scans with combined scan ranges for each present mode. 
# @author Jasen Finch
#' @importFrom plyr ldply

combScans <- function(x,scans,sranges,modes){
	# separate scans based on modes
	pat <- unlist(lapply(modes,function(x,sranges){
		rep(x,length(sranges))
	},sranges = sranges))
	pat <- rep(pat,length(x)/length(pat))
	pos.neg <- lapply(modes,function(y,x,pat){
		x <- x[which(pat == y)]
		return(x)
	},pat = pat,x = x)
	# separate scan ranges and keep only relevant scans
	pat.1 <- unlist(lapply(seq(1,length(pos.neg[[1]])/length(sranges)),rep,times = length(sranges)))
	pos.neg <- lapply(pos.neg,function(x,pattern){
		y <- list()
		for (i in unique(pattern)) {
			y[[i]] <- x[which(pattern == i)]
		}
		return(y)
	},pattern = pat.1)
	pos.neg <- lapply(pos.neg,function(x,scans){
		return(x[scans])
	},scans = scans)
	# combine scan ranges into single lists, boundary always equal to upper limit
	pos.neg <- lapply(pos.neg,function(x,sranges){
		return(lapply(x,function(y,sranges){
			for (i in 1:length(y)) {
				z <- y[[i]]
				y[[i]] <- z[which(z[,1] > sranges[[i]][1] & z[,1] <= sranges[[i]][2]),]
			}
			y <- ldply(y,data.frame)
			colnames(y) <- c("mz","intensity")
			return(y)
		},sranges = sranges))},sranges = sranges)
	pos.neg <- lapply(pos.neg,function(x,scans){
		names(x) <- scans
		return(x)
	},scans = scans)
	names(pos.neg) <- modes
	return(pos.neg)
	}