--- a/GRsetFromGEO/GRsetFromGEO.R	Mon Apr 24 08:50:59 2017 -0400
+++ b/GRsetFromGEO/GRsetFromGEO.R	Mon Apr 24 08:57:06 2017 -0400
@@ -21,44 +21,47 @@
 
 
 
-function (GSE = GSE, array = "IlluminaHumanMethylation450k", annotation = default.450k.annotation,
-          what = c("Beta", "M"), mergeManifest = FALSE, i = 1){
-  
-  
-  gset <- getGEO(GSE)
-  gset <- gset[[1]]
-  
-  platform <- annotation(gset)
-  
-  ann <- getAnnotationString(c(array = array, annotation = annotation))
-  if (!require(ann, character.only = TRUE)) 
-    stop(sprintf("cannot load annotation package %s", ann))
-  
-  object <- get(ann)
-  
-  gr <- getLocations(object, mergeManifest = mergeManifest, 
-                     orderByLocation = TRUE)
-  locusNames <- names(gr)
-  sampleNames(gset) <- gset$title
-  common <- intersect(locusNames, fData(gset)$Name)
-  if (length(common) == 0) {
-    stop("No rowname matches. 'rownames' need to match IlluminaHumanMethylation450k probe names.")
-    ind1 <- match(common, fData(gset)$Name)
-    ind2 <- match(common, locusNames)
-    preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details"))
-    if (what == "Beta") {
-      out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1, 
-                                                                 , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset), 
-                             annotation = c(array = array, annotation = annotation), 
-                             preprocessMethod = preprocessing)
-    }
-    else {
-      out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL, 
-                             M = exprs(gset)[ind1, , drop = FALSE], CN = NULL, 
-                             pData = pData(gset), annotation = c(array = array, 
-                                                                 annotation = annotation), preprocessMethod = preprocessing)
-    }
-    return(out)
+array = "IlluminaHumanMethylation450k"
+annotation = default.450k.annotation
+what = c("Beta", "M")
+mergeManifest = FALSE
+i = 1
+
+gset <- getGEO(GSE)
+gset <- gset[[1]]
+
+platform <- annotation(gset)
+
+ann <- getAnnotationString(c(array = array, annotation = annotation))
+if (!require(ann, character.only = TRUE)) 
+  stop(sprintf("cannot load annotation package %s", ann))
+
+object <- get(ann)
+
+gr <- getLocations(object, mergeManifest = mergeManifest, 
+                   orderByLocation = TRUE)
+locusNames <- names(gr)
+sampleNames(gset) <- gset$title
+common <- intersect(locusNames, fData(gset)$Name)
+if (length(common) == 0) {
+  stop("No rowname matches. 'rownames' need to match IlluminaHumanMethylation450k probe names.")
+  ind1 <- match(common, fData(gset)$Name)
+  ind2 <- match(common, locusNames)
+  preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details"))
+  if (what == "Beta") {
+    out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1, 
+                                                               , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset), 
+                           annotation = c(array = array, annotation = annotation), 
+                           preprocessMethod = preprocessing)
   }
-  save(out,file = output)
+  else {
+    out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL, 
+                           M = exprs(gset)[ind1, , drop = FALSE], CN = NULL, 
+                           pData = pData(gset), annotation = c(array = array, 
+                                                               annotation = annotation), preprocessMethod = preprocessing)
+  }
+  return(out)
 }
+save(out,file = output)
+
+