wEIC: R package for extract EIC from mzXML

# @title
#LCreat
#
# @ description
#creat list and filter ;preparation for EIC
# @para
#InL=1000 <intensity low limited>
#StT=0 <start time>
#EnT  <end time>
#DPa <data path>
#DNa <data name>
#LNa <list name>
#msn <MSLevel>
#@return
#LNa as list
# Some useful keyboard shortcuts for package authoring:
#
#   Build and Reload Package:  'Ctrl + Shift + B'
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#,backend = "Ramp"
LCreat <- function(DNalis,InL,StT,EnT,MSn=1) {
  require(mzR);
  if (missing(DNalis)) {DNalis<-list.files(getwd(),pattern="mzXML")} else {}
  mzOb<-list()
  DPa<-getwd()

  for (jj in 1 : length(DNalis)) {
    DNa<-DNalis[jj]
    file<-list.files(DPa,pattern =DNa,full.names = TRUE,recursive =FALSE);
    aa<-openMSfile(file);
    LNa<-peaks(aa);
    rtna<-header(aa);
    rtna$msLevel[rtna$msLevel!=MSn]<-NA
    rtna<-rtna[-23]
    rtna<-na.omit(rtna)
    rtna$retentionTime<-rtna$retentionTime/60

    if (missing(StT) | missing(EnT)) {} else {
      rtna$retentionTime[rtna$retentionTime<StT]<-NA
      rtna$retentionTime[rtna$retentionTime>EnT]<-NA}
    rtna<-na.omit(rtna)
    LNa<-LNa[rtna$seqNum]

    names(LNa)<-rtna$retentionTime
    ScNu<-as.numeric(length(LNa))
    if (missing(InL)) {} else {
      n=0;detL=0;oriL<-length(LNa);for (i in 1 : length(LNa)) {LNa[[i-detL]][,2][LNa[[i-detL]][,2]<InL]<-NA;detL<-oriL-length(LNa)}
      n=0;detL=0;oriL<-length(LNa);for (i in 1 : length(LNa)) {LNa[[i-detL]]<-na.omit(LNa[[i-detL]]);detL<-oriL-length(LNa)}}
    mzOb[[jj]]<-LNa
  }
  names(mzOb)<-DNalis
  save(mzOb,file = "mzOb.RDa")
  return()
}