R/fastMatchPpm.R

In proFIA: Preprocessing of FIA-HRMS data

fastMatchPpm <- function(x,y,ppm=3, symmetric=FALSE) {
  
  if (any(is.na(y)))
    stop("NA's are not allowed in y !\n")
  ok <- !(is.na(x))
  ans <- order(x)
  keep <- seq_along(ok)[ok]
  xidx <- ans[ans %in% keep]
  xs <- x[xidx]
  yidx <- order(y)
  ys <- y[yidx]
  if (!is.double(xs))
    xs <- as.double(xs)
  if (!is.double(ys))
    ys<- as.double(ys)
  if (!is.integer(xidx))
    xidx <- as.integer(xidx)
  if (!is.integer(yidx))
    yidx <- as.integer(yidx)
  
  fm <- .Call("matchPpm", xs, ys, xidx, yidx, as.integer(length(x)), as.double(ppm),PACKAGE = "proFIA")
  fm2 <- vector("list", length=length(fm))
  ##stop("!")
  if (symmetric){
    for (a in 1:length(fm)) {
      if (!is.null(fm[[a]][1])){
        tmp<-NULL
        for (b in 1:length(fm[[a]])){
          if ((abs(x[a]-y[fm[[a]]][b]) == min(abs(x[a]-y[fm[[a]][b]]),
                                              abs(x[a]  -y[fm[[a]][b]-1]),
                                              abs(x[a]  -y[fm[[a]][b]+1]),
                                              abs(x[a-1]-y[fm[[a]][b]]),
                                              abs(x[a+1]-y[fm[[a]][b]]), na.rm=TRUE)
          )) {
            tmp<-c(tmp, fm[[a]][b])
          }
        }
        fm2[[a]]<-tmp
      }
    }
  }else {
    fm2 <- fm}
  fm2
}