--- a/averageFragSpectra.R	Tue Feb 08 13:54:03 2022 +0000
+++ b/averageFragSpectra.R	Wed Jun 12 16:01:28 2024 +0000
@@ -5,30 +5,28 @@
 
 
 get_av_spectra <- function(x) {
-
   if (length(x$av_intra) > 0) {
     av_intra_df <- plyr::ldply(x$av_intra)
 
     if (nrow(av_intra_df) == 0) {
       av_intra_df <- NULL
-    }else{
+    } else {
       av_intra_df$method <- "intra"
     }
-
-  }else{
+  } else {
     av_intra_df <- NULL
   }
 
   if ((is.null(x$av_inter)) || (nrow(x$av_inter) == 0)) {
     av_inter_df <- NULL
-  }else{
+  } else {
     av_inter_df <- x$av_inter
     av_inter_df$method <- "inter"
   }
 
   if ((is.null(x$av_all)) || (nrow(x$av_all) == 0)) {
     av_all_df <- NULL
-  }else{
+  } else {
     av_all_df <- x$av_all
     av_all_df$method <- "all"
   }
@@ -60,9 +58,9 @@
 
 
 load_r_data <- function(rdata_path, name) {
-    #loads an RData file, and returns the named xset object if it is there
-    load(rdata_path)
-    return(get(ls()[ls() %in% name]))
+  # loads an RData file, and returns the named xset object if it is there
+  load(rdata_path)
+  return(get(ls()[ls() %in% name]))
 }
 
 # Requires
@@ -72,59 +70,58 @@
 
 if (is.null(opt$rmp)) {
   rmp <- FALSE
-}else{
+} else {
   rmp <- TRUE
 }
 
 if (is.null(opt$sumi)) {
   sumi <- FALSE
-}else{
+} else {
   sumi <- TRUE
 }
 
 if (opt$av_level == "intra") {
   pa <- msPurity::averageIntraFragSpectra(pa,
-                                          minfrac = opt$minfrac,
-                                          minnum = opt$minnum,
-                                          ppm = opt$ppm,
-                                          snr = opt$snr,
-                                          ra = opt$ra,
-                                          av = opt$av,
-                                          sumi = sumi,
-                                          rmp = rmp,
-                                          cores = opt$cores)
-
+    minfrac = opt$minfrac,
+    minnum = opt$minnum,
+    ppm = opt$ppm,
+    snr = opt$snr,
+    ra = opt$ra,
+    av = opt$av,
+    sumi = sumi,
+    rmp = rmp,
+    cores = opt$cores
+  )
 } else if (opt$av_level == "inter") {
-
   pa <- msPurity::averageInterFragSpectra(pa,
-                                          minfrac = opt$minfrac,
-                                          minnum = opt$minnum,
-                                          ppm = opt$ppm,
-                                          snr = opt$snr,
-                                          ra = opt$ra,
-                                          av = opt$av,
-                                          sumi = sumi,
-                                          rmp = rmp,
-                                          cores = opt$cores)
+    minfrac = opt$minfrac,
+    minnum = opt$minnum,
+    ppm = opt$ppm,
+    snr = opt$snr,
+    ra = opt$ra,
+    av = opt$av,
+    sumi = sumi,
+    rmp = rmp,
+    cores = opt$cores
+  )
 } else if (opt$av_level == "all") {
-
   pa <- msPurity::averageAllFragSpectra(pa,
-                                        minfrac = opt$minfrac,
-                                        minnum = opt$minnum,
-                                        ppm = opt$ppm,
-                                        snr = opt$snr,
-                                        ra = opt$ra,
-                                        av = opt$av,
-                                        sumi = sumi,
-                                        rmp = rmp,
-                                        cores = opt$cores)
+    minfrac = opt$minfrac,
+    minnum = opt$minnum,
+    ppm = opt$ppm,
+    snr = opt$snr,
+    ra = opt$ra,
+    av = opt$av,
+    sumi = sumi,
+    rmp = rmp,
+    cores = opt$cores
+  )
 }
 
 print(pa)
 save(pa, file = opt$out_rdata)
 
 if (length(pa) > 0) {
-
   av_spectra <- plyr::ldply(pa@av_spectra, get_av_spectra)
 
   if (nrow(av_spectra) == 0) {
@@ -138,18 +135,20 @@
       colnames(av_spectra)[2] <- "fileid"
       av_spectra$avid <- seq_len(nrow(av_spectra))
 
-      filenames <- sapply(av_spectra$fileid,
-                          function(x) names(pa@fileList)[as.integer(x)])
+      filenames <- sapply(
+        av_spectra$fileid,
+        function(x) names(pa@fileList)[as.integer(x)]
+      )
       # filenames_galaxy <- sapply(
       #    av_spectra$fileid, function(x) basename(pa@fileList[as.integer(x)]))
 
-        av_spectra <- as.data.frame(
-          append(av_spectra, list(filename = filenames), after = 2))
+      av_spectra <- as.data.frame(
+        append(av_spectra, list(filename = filenames), after = 2)
+      )
     }
 
 
     print(head(av_spectra))
     write.table(av_spectra, opt$out_peaklist, row.names = FALSE, sep = "\t")
-
   }
 }