R/misc.R

In jcapelladesto/isoSCAN: Automatic Integration for GC-CI-MS Isotope Labeling Data

calc.Res <- function(R,m,mz){ R*sqrt(m/mz)}

ppmDiff <- function(a,b){ abs(a-b)*1e6/b }

rmfileExt <- function(x,ext.regexp){
  x <- basename(x)
  x <- gsub(ext.regexp,"",x)
  return(x)
}

decompose.formula <- function(formula){
  rgm <- gregexpr("[A-Z]",formula)[[1]]
  rgm <- as.numeric(rgm)
  r <- sapply(1:length(rgm),function(i){
    j <- rgm[i]
    if(rgm[i+1]%in%rgm){
      ele <-  substring(formula,j,j)
      num <- substring(formula,j+1,rgm[i+1]-1)
      if(is.na(num)){num <- substring(formula,j+1,nchar(formula))}
    }else{
      if(grepl("[0-9]",substring(formula,j+1,j+1))){
        ele <- substring(formula,j,j)
        num <- substring(formula,j+1,rgm[i+1]-1)
        if(is.na(num)){num <- substring(formula,j+1,nchar(formula))}
      }else{
        ele <- substring(formula,j,j+1)
        num <- substring(formula,j+2,rgm[i+1]-1)
        if(is.na(num)){num <- substring(formula,j+2,nchar(formula))}
      }
      
    }
    if(num==""){num <- 1}
    return(c(ele,num))
  })
  Element <- r[1,]
  Number <- r[2,]
  r <- data.frame(Element,Number,stringsAsFactors = F)  
  # colnames(r) <- c("Element","Number")
  rownames(r) <- NULL
  return(r)
}

iso.generator <- function (formula, atom, nisos, isotopes) {
	
	#DETECT CHARGE I AFEGIR AL FINAL DESPRES DE FER ELS ISOS
	isCharged <- F
	if(grepl("(\\+)",formula)){
		isCharged <- T
		charge <- "+"
		formula <- gsub("(\\+)","",formula)
	}
	
	if(grepl("(\\-)",formula)){
		isCharged <- T
		charge <- "-"
		formula <- gsub("(\\-)","",formula)
	}
	
	isos <- isotopes[which(isotopes$isotope == atom), ]
	isos <- isos[grep("\\[", isos$element), ]
	isoel <- gsub("[0-9]", "", atom)
	decform <- isoSCAN:::decompose.formula(formula)
	isoidx <- which(decform$Element == isoel)
	isoeln <- as.numeric(decform$Number[isoidx])
	decform <- decform[-isoidx, ]
	newiso <- isoeln - nisos
	newiso <- sapply(newiso, function(x) {
		if (x > 0) {
			paste0(isoel, x)
		}
		else {
			""
		}
	})
	varvec <- paste0(paste0(isos$element, nisos), newiso)
	fixed <- paste(sapply(1:nrow(decform), function(x) paste0(decform[x, 
	], collapse = "")), collapse = "")
	res <- paste0(varvec, fixed)
	res <- c(formula, res)
	if(isCharged){
		res <- paste0(res,charge)
	}
	return(res)
}

countDecimalPlaces <- function(x) { 
  #from stackoverflow fvfaleiro
  if ((x %% 1) != 0) {
    strs <- strsplit(as.character(format(x, scientific = F)), "\\.")
    n <- nchar(strs[[1]][2])
  } else {
    n <- 0
  }
  return(n) 
}