--- a/flag-remove-peaks.R	Wed Jul 18 06:04:14 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,191 +0,0 @@
-library(msPurity)
-library(optparse)
-print(sessionInfo())
-option_list <- list(
-  make_option(c("-o", "--out_dir"), type="character", default=getwd(),
-              help="Output folder for resulting files [default = %default]"
-  ),
-  make_option(c("-x", "--xset_path"), type="character", default=file.path(getwd(),"xset.rds"),
-              help="The path to the xcmsSet object [default = %default]"
-  ),
-  make_option("--polarity", default=NA,
-              help="polarity (just used for naming purpose for files being saved) [positive, negative, NA] [default %default]"
-  ),
-  make_option("--rsd_i_blank", default=100,
-              help="RSD threshold for the blank [default = %default]"
-  ),
-  make_option("--minfrac_blank", default=0.5,
-              help="minimum fraction of files for features needed for the blank [default = %default]"
-  ),
-  make_option("--rsd_rt_blank", default=100,
-              help="RSD threshold for the RT of the blank [default = %default]"
-  ),
-
-  make_option("--ithres_blank", default=0,
-              help="Intensity threshold for the blank [default = %default]"
-  ),
-  make_option("--s2b", default=10,
-              help="fold change (sample/blank) needed for sample peak to be allowed. e.g.
-                    if s2b set to 10 and the recorded sample 'intensity' value was 100 and blank was 10.
-                    1000/10 = 100, so sample has fold change higher than the threshold and the peak
-                    is not considered a blank [default = %default]"
-  ),
-  make_option("--blank_class", default='blank', type="character",
-              help="A string representing the class that will be used for the blank.[default = %default]"
-  ),
-  make_option("--egauss_thr", default=NA,
-              help="Threshold for filtering out non gaussian shaped peaks. Note this only works
-                            if the 'verbose columns' and 'fit gauss' was used with xcms
-                            [default = %default]"
-  ),
-  make_option("--rsd_i_sample", default=100,
-              help="RSD threshold for the samples [default = %default]"
-  ),
-  make_option("--minfrac_sample", default=0.8,
-              help="minimum fraction of files for features needed for the samples [default = %default]"
-  ),
-  make_option("--rsd_rt_sample", default=100,
-              help="RSD threshold for the RT of the samples [default = %default]"
-  ),
-  make_option("--ithres_sample", default=5000,
-              help="Intensity threshold for the sample [default = %default]"
-  ),
-  make_option("--grp_rm_ids", default=NA,
-              help="vector of grouped_xcms peaks to remove (corresponds to the row from xcms::group output)
-              [default = %default]"
-  ),
-  make_option("--remove_spectra",  action="store_true",
-              help=" TRUE if flagged spectra is to be removed [default = %default]"
-  ),
-  make_option("--minfrac_xcms", default=0.5,
-              help="minfrac for xcms  grouping [default = %default]"
-  ),
-  make_option("--mzwid", default=0.001,
-              help="mzwid for xcms  grouping [default = %default]"
-  ),
-  make_option("--bw", default=5,
-              help="bw for xcms  grouping [default = %default]"
-  ),
-
-  make_option("--temp_save",  action="store_true",
-              help="Assign True if files for each step saved (for testing purposes) [default = %default]"
-  ),
-
-  make_option("--samplelist",  type="character", help="Sample list to determine the blank class"),
-
-  make_option("--xset_name",  default="xset",
-              help="Name of the xcmsSet object within the RData file [default = %default]"
-  )
-
-
-
-)
-
-  #make_option("--multilist", action="store_true"
-  #            help="NOT CURRENTLY IMPLEMENTED: If paired blank removal is to be performed a - multilist -  sample list file has to be provided"
-  #),
-
-# store options
-opt<- parse_args(OptionParser(option_list=option_list))
-
-opt <- replace(opt, opt == "NA", NA)
-
-
-
-
-if (is.null(opt$temp_save)){
-    temp_save<-FALSE
-}else{
-    temp_save<-TRUE
-}
-
-if (is.null(opt$remove_spectra)){
-    remove_spectra<-FALSE
-}else{
-    remove_spectra<-TRUE
-}
-
-
-print(opt)
-
-loadRData <- function(rdata_path, xset_name){
-#loads an RData file, and returns the named xset object if it is there
-    load(rdata_path)
-    return(get(ls()[ls() == xset_name]))
-}
-
-xset<-loadRData(opt$xset_path, opt$xset_name)
-print(xset)
-if (is.null(opt$samplelist)){
-    blank_class <- opt$blank_class
-}else{
-    samplelist <- read.table(opt$samplelist, sep='\t', header=TRUE)
-    samplelist_blank <- unique(samplelist$sample_class[samplelist$blank=='yes'])
-
-    chosen_blank <- samplelist_blank[samplelist_blank %in% xset@phenoData$class]
-    if (length(chosen_blank)>1){
-        print('ERROR: only 1 blank is currently allowed to be used with this tool')
-        exit()
-    }
-    blank_class <- as.character(chosen_blank)
-    print(blank_class)
-}
-
-
-if (is.null(opt$multilist)){
-    ffrm_out <- flag_remove(xset,
-                        pol=opt$polarity,
-                        rsd_i_blank=opt$rsd_i_blank,
-                        minfrac_blank=opt$minfrac_blank,
-                        rsd_rt_blank=opt$rsd_rt_blank,
-                        ithres_blank=opt$ithres_blank,
-                        s2b=opt$s2b,
-                        ref.class=blank_class,
-                        egauss_thr=opt$egauss_thr,
-                        rsd_i_sample=opt$rsd_i_sample,
-                        minfrac_sample=opt$minfrac_sample,
-                        rsd_rt_sample=opt$rsd_rt_sample,
-                        ithres_sample=opt$ithres_sample,
-                        minfrac_xcms=opt$minfrac_xcms,
-                        mzwid=opt$mzwid,
-                        bw=opt$bw,
-                        out_dir=opt$out_dir,
-                        temp_save=temp_save,
-                        remove_spectra=remove_spectra,
-                        grp_rm_ids=unlist(strsplit(as.character(opt$grp_rm_ids), split=", "))[[1]])
-    print('flag remove finished')
-    xset <- ffrm_out[[1]]
-    grp_peaklist <- ffrm_out[[2]]
-    removed_peaks <- ffrm_out[[3]]
-
-    save.image(file=file.path(opt$out_dir, 'xset_filtered.RData'))
-
-    # grpid needed for mspurity ID needed for deconrank... (will clean up at some up)
-    peak_pth <- file.path(opt$out_dir, 'peaklist_filtered.tsv')
-    print(peak_pth)
-    write.table(data.frame('grpid'=rownames(grp_peaklist), 'ID'=rownames(grp_peaklist), grp_peaklist),
-                peak_pth, row.names=FALSE, sep='\t')
-
-    removed_peaks <- data.frame(removed_peaks)
-    write.table(data.frame('ID'=rownames(removed_peaks),removed_peaks),
-        file.path(opt$out_dir, 'removed_peaks.tsv'), row.names=FALSE, sep='\t')
-
-}else{
-
-   
-   # TODO
-   #xsets <- split(xset, multilist_df$multlist)
-   #
-   #mult_grps <- unique(multilist_df$multlist)
-   #
-   #for (mgrp in mult_grps){
-   #   xset_i <- xsets[mgrp]
-   #   xcms::group(xset_i, 
-   #
-   # }
-
-
-
-}
-
-