changeset 35:694382fd220a draft

Uploaded

--- a/GRsetFromGEO/GRsetFromGEO.R	Fri Apr 14 09:25:08 2017 -0400
+++ b/GRsetFromGEO/GRsetFromGEO.R	Fri Apr 14 14:16:46 2017 -0400
@@ -4,6 +4,57 @@
 GSE = args[1] 
 output = args[2] 
 
-GRset <- getGenomicRatioSetFromGEO(GSE)
-
-save(GRset,output)
\ No newline at end of file
+function (GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k", 
+          annotation = .default.450k.annotation, what = c("Beta", "M"), 
+          mergeManifest = FALSE, i = 1) 
+{
+  what <- match.arg(what)
+  if (is.null(GSE) && is.null(path)) 
+    stop("Either GSE or path must be supplied.")
+  if (!is.null(GSE)) 
+    gset <- GEOquery::getGEO(GSE)
+  else gset <- GEOquery::getGEO(filename = file.path(path, 
+                                                     list.files(path, pattern = ".soft")))
+  if (length(gset) == 0) 
+    stop("Empty list retrieved from GEO.")
+  if (length(gset) > 1) {
+    warning("More than one ExpressionSet found:\n", names(gset), 
+            "\nUsing entry ", i)
+    gset <- gset[[i]]
+  }
+  else gset <- gset[[1]]
+  platform <- annotation(gset)
+  if (platform != "GPL13534") 
+    warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.", 
+                    platform))
+  if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) < 
+                        0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1)) 
+    warning("Values outside [0,1] detected. 'what' argument should not be Beta.")
+  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)
+  }
+  save(out,output)
+}