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#' Filters a list of fcs files by search terms
#This function returns a filtered list of fcs files of interest from a larger list
#It takes the list of file IDs with FCS file names as names (files), and one or more strings of interest as a list to filter samples(string)
#It may be used to filter samples by pt/control status or stimulation.
#It returns a list of sample IDs with their names meeting filtering criteria
#' @param files - List of fcs file IDs with FCS file name as names for list
#' @param string - List of one or more strings of interest as a list to filter samples
#' @return Returns a list of file IDs matching with names matching string(s)
#' @examples \donttest{
#' #Example starting with obtaining data from Cytobank
#' library(CytobankAPI)
#' exptno<-4
#' cyto_session <- authenticate(site="premium", username="myusername", password="mypassword")
#' files<-getfcsfiles(exptno,cyto_session)
#' string<-c("patient","IL-1b")
#' filterfiles(file,string)}
#'
#' #Simple example when list of file names is already available
#' files<-1:4
#' names(files)<-c("Pt1 unst.fcs","Pt2 stim.fcs","Ctrl1 unst.fcs","Ctrl2 stim.fcs")
#' #Filtering file list to contain only unstimulated files
#' filterfiles(files,"unstimulated")
#' #Filtering file list to contain only patient files
#' filterfiles(files,"Pt")
#' #Filtering file list to contain both unstimulated and patient files
#' filterfiles(files,c("Pt","unst"))
#' @export
filterfiles<-function(files,string){
ind=vector()
for(x in string){
ind=union(ind,grep(x,names(files)))
}
ind=sort(ind)
filtered=files[ind]
return(filtered)
}
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