R/process_query.R

In daniellyz/MergeION2: Merging and Networking Scans from Multiple LC-MS/MS Raw Data Files

#' Searching and managing the spectral library
#'
#' The function is used by library_query() to select scans based on a query expression.
#'
#' @param query query expression - two ways to specify drop
#' @param setString string used to seperate paramter name and expression
#' \itemize{
#'\item{equal:}{use e.g. 'IONMODE=Positive' to do exact search}
#' \item{regex:}{use e.g. 'IONMODE@xxx@^Pos' to search IONMODE begins with 'Pos'}
#'}
#' @export
#'
#' @importFrom stringr str_replace_all fixed str_detect
#'

process_query<-function(library0, query = "", ppm_search = 20, rt_search = 12, sepString = "@xxx@"){
	
	options(stringsAsFactors = FALSE)
	options(warn=-1)
	
	#####################################
	### Reading from spectral library:###
	#####################################
	
	metadata = library0$metadata
	spectrum_list = library0$sp
	
	prec_mz = as.numeric(metadata$PEPMASS)
	prec_rt = as.numeric(metadata$RT)
	
	#############################################
	### Run query expressions and find indexes ##
	#############################################
	
	if (!is.character(query)){
		stop("Query expression is not valid!")}
	
	if (all(query!="") & (length(query) > 0)){
		
		indexes_list = list()
		NI = 0
		
		for (eps in query){
			
			# Search pepmass and rt:
			
			eps1 =  str_replace_all(eps,fixed(" "),"") # Remove white space
			
# if exact search
			if(str_detect(eps1, "=")){
				
				if (startsWith(eps1,"PEPMASS=")){
					target_mass = as.numeric(strsplit(eps1,"=")[[1]][2])
					if (!is.na(target_mass)){
						ppm_list = ppm_distance(prec_mz, target_mass)
						indexes = which(ppm_list<=ppm_search)
					}
				} else if (startsWith(eps1,"RT=")){
					target_rt = as.numeric(strsplit(eps1,"=")[[1]][2])
					if (!is.na(target_rt)){
						rtdev_list = abs(target_rt*60-prec_rt*60)
						indexes = which(rtdev_list<=rt_search)
					}} else {
					
					# Search other things:
					target_variable = strsplit(eps,"=")[[1]][1]
					target_value = gsub(paste0(target_variable,"="), "", eps)
					target_variable = trimws(target_variable)
					target_value = trimws(target_value)
					
					cid = which(colnames(metadata) == target_variable)
					if (length(cid) == 1){
						indexes = which(metadata[,cid]==target_value)}
				}
			}else{
				# here we apply fuzzy search in R
				target_variable = trimws(strsplit(eps, sepString)[[1]][1])
				target_expression = strsplit(eps, sepString)[[1]][2]
				indexes = which(grepl( target_expression, metadata[, target_variable,drop = TRUE], ignore.case = TRUE))
				#grep( target_expression, metadata[, target_variable], value = T)
			}
			
			# Add valid indexes:
			
			if (length(indexes)>0){
				NI = NI + 1
				indexes_list[[NI]] = indexes}
		} #end of for loop
		
		indexes_list = Reduce(intersect,indexes_list)
	} # end of if query not empty
	else{
	  
	  indexes_list  <- 1:nrow(metadata)
	}
	# Output results:
	
	NN = 1:length(spectrum_list)
	left_list = setdiff(NN, indexes_list)
	
	SELECTED_LIBRARY = LEFT_LIBRARY = library0
	SELECTED_LIBRARY$sp = library0$sp[indexes_list]
	SELECTED_LIBRARY$metadata = library0$metadata[indexes_list,,drop=FALSE]
	LEFT_LIBRARY$sp = library0$sp[left_list]
	LEFT_LIBRARY$metadata = library0$metadata[left_list,,drop=FALSE]
	
	return(list(SELECTED = SELECTED_LIBRARY,
					LEFT = LEFT_LIBRARY))
}

#########################
### Internal functions:##
#########################

# ppm error calculation:

ppm_distance<-function(x,y){
	x = as.numeric(x)
	y = as.numeric(y)
	if (y>100){
		ppm = abs((x-y))/y*1000000
	} else {
		ppm = abs(x-y)
		ppm[ppm<0.01]=0
	}
	return(ppm)
}