diff findDMR/.Rhistory @ 10:7df2b7d79391 draft

Uploaded

--- a/findDMR/.Rhistory	Tue Apr 25 13:35:53 2017 -0400
+++ b/findDMR/.Rhistory	Thu May 11 11:15:33 2017 -0400
@@ -1,1 +1,200 @@
-??fread
+clusterSize=2
+class(clusterSize)
+type(clusterSize)
+require("minfi", quietly = TRUE)
+??getGenomicRatioSetFromGEO
+getGenomicRatioSetFromGEO
+getwd()
+GEODataTable <- getGEO(GSE51547)
+require("BiocGenerics", quietly = TRUE)
+require("data.table", quietly = TRUE)
+require("GEOquery", quietly = TRUE)
+require("rtracklayer", quietly = TRUE)
+require("FDb.InfiniumMethylation.hg19", quietly = TRUE)
+GEODataTable <- getGEO(GSE51547)
+GEODataTable <- getGEO("GSE51547")
+IlmnIDTable <- Table(GEODataTable)
+MetaData <- data.frame(Meta(GEODataTable))
+IlmnIDTable <- Table(GEODataTable)
+GEODataTable
+GSE<-"GSE51547"
+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)$Name)
+ind2 <- match(common, locusNames)
+preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details"))
+if (what == "Beta") {
+out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1,
+, drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
+annotation = c(array = array, annotation = annotation),
+preprocessMethod = preprocessing)
+}
+else {
+out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL,
+M = exprs(gset)[ind1, , drop = FALSE], CN = NULL,
+pData = pData(gset), annotation = c(array = array,
+annotation = annotation), preprocessMethod = preprocessing)
+}
+return(out)
+}
+<environment: namespace:minfi>
+function (GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k",
+annotation = .default.450k.annotation, what = c("Beta", "M"),
+mergeManifest = FALSE, i = 1)
+{
+what <- match.arg(what)
+if (is.null(GSE) && is.null(path))
+stop("Either GSE or path must be supplied.")
+if (!is.null(GSE))
+gset <- GEOquery::getGEO(GSE)
+else gset <- GEOquery::getGEO(filename = file.path(path,
+list.files(path, pattern = ".soft")))
+if (length(gset) == 0)
+stop("Empty list retrieved from GEO.")
+if (length(gset) > 1) {
+warning("More than one ExpressionSet found:\n", names(gset),
+"\nUsing entry ", i)
+gset <- gset[[i]]
+}
+else gset <- gset[[1]]
+platform <- annotation(gset)
+if (platform != "GPL13534")
+warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.",
+platform))
+if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <
+0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1))
+warning("Values outside [0,1] detected. 'what' argument should not be Beta.")
+ann <- .getAnnotationString(c(array = array, annotation = annotation))
+if (!require(ann, character.only = TRUE))
+stop(sprintf("cannot load annotation package %s", ann))
+object <- get(ann)
+gr <- getLocations(object, mergeManifest = mergeManifest,
+orderByLocation = TRUE)
+locusNames <- names(gr)
+sampleNames(gset) <- gset$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)
+}
+return(out)
+}
+GSE<-"GSE51547"
+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)$Name)
+ind2 <- match(common, locusNames)
+preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details"))
+if (what == "Beta") {
+out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1,
+, drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
+annotation = c(array = array, annotation = annotation),
+preprocessMethod = preprocessing)
+}
+else {
+out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL,
+M = exprs(gset)[ind1, , drop = FALSE], CN = NULL,
+pData = pData(gset), annotation = c(array = array,
+annotation = annotation), preprocessMethod = preprocessing)
+}
+return(out)
+}
+out
+GSE<-"GSE51547"
+gset <- getGEO(GSE)
+ann <- .getAnnotationString(c(array = array, annotation = annotation))
+platform <- annotation(gset)
+hm450.hg19 <- getPlatform()
+IlmnInfo <-
+data.table(
+IlmnID = names(hm450.hg19),
+CHR = as.data.frame(hm450.hg19@seqnames)$value,
+BP = as.numeric(hm450.hg19@elementMetadata$probeStart)
+)
+IlmnIDTable <- Table(gset)
+??getGenomicRatioSetFromGEO()
+getGenomicRatioSetFromGEO()
+getGenomicRatioSetFromGEO