In Pohnert-Lab/DeltaMS: Isotopologue finder

$\Delta$ m = r isoD@isotopeMassDiff

Charge for desired ions was set to r isoD@charge.

Analyzed files:

if(isoD@TypeofExp==1){
options(knitr.kable.NA = "")
namesFolder<-basename(isoD@WD)
filesInfolders<-list.files(isoD@WD, pattern = isoD@MSfilePattern, ignore.case = TRUE)
df<-data.frame(filesInfolders)
names(df)<-paste0(namesFolder,"*")
knitr::kable(df, format = "markdown", row.names = FALSE,align = "c", caption = NULL)
}

if(isoD@TypeofExp==2){
options(knitr.kable.NA = "")
namesFolder<-c(isoD@unLabeledS,isoD@LabeledS)
folderpaths<-as.list(file.path(isoD@WD, namesFolder))
filesInfolders<-lapply(folderpaths, function(i) {list.files(i, pattern = isoD@MSfilePattern, ignore.case = TRUE)})
names(filesInfolders)<-c("unlabeled Samples", "labeled Samples")
filesInfolders<-lapply(filesInfolders, `length<-`, max(lengths(filesInfolders)))
foldertable<-as.data.frame(filesInfolders, optional = TRUE)
foldertableM<-as.matrix(foldertable)
foldertableM<-rbind(paste0(namesFolder,"*"), foldertableM)
knitr::kable(foldertableM, format = "markdown", row.names = FALSE,align = "c", caption =NULL)
  }

if(isoD@TypeofExp==3){
options(knitr.kable.NA = "")
namesFolder<-c(isoD@uC,isoD@lC,isoD@uT,isoD@lT)
folderpaths<-as.list(file.path(isoD@WD, namesFolder))
filesInfolders<-lapply(folderpaths, function(i) {list.files(i, pattern = isoD@MSfilePattern, ignore.case = TRUE)})
names(filesInfolders)<-c("unlabeled Control", "labeled Control", "unlabeled Treatment", "labeled Treatment")
filesInfolders<-lapply(filesInfolders, `length<-`, max(lengths(filesInfolders)))
foldertable<-as.data.frame(filesInfolders, optional = TRUE)
foldertableM<-as.matrix(foldertable)
foldertableM<-rbind(paste0(namesFolder,"*"), foldertableM)
knitr::kable(foldertableM, format = "markdown", row.names = FALSE,align = "c", caption =NULL)
}