--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getGEO/test-data/.Rhistory	Tue Apr 25 10:28:34 2017 -0400
@@ -0,0 +1,512 @@
+what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <
+0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1)
+??getLocations
+sampleNames(gset) <- gset$title
+if (platform != "GPL13534")
+warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.",
+platform))
+if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <
+0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1))
+warning("Values outside [0,1] detected. 'what' argument should not be Beta.")
+ann <- .getAnnotationString(c(array = array, annotation = annotation))
+if (!require(ann, character.only = TRUE))
+stop(sprintf("cannot load annotation package %s", ann))
+getGenomicRatioSetFromGEO
+object <- get(platform)
+platform
+gr <- getLocations(gset, mergeManifest = mergeManifest,
+orderByLocation = TRUE)
+gr <- getLocations(gset)
+gset
+gr <- getLocations(platform)
+??getLocations
+locusNames <- names(gset)
+sampleNames(gset) <- gset$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)
+}
+what
+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)
+out <- GenomicRatioSet(gr = gset[ind2, ], Beta = exprs(gset)[ind1,
+, drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
+annotation = c(array = array, annotation = annotation),
+preprocessMethod = preprocessing)
+ind2
+ind1
+common
+sampleNames(gset)
+class(gmSet)
+out <- GenomicRatioSet(gr = gmset, Beta = exprs(gset)[ind1,
+, drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
+annotation = c(array = array, annotation = annotation),
+preprocessMethod = preprocessing)
+if (length(TAB$ID) > 1) {
+mysamples <-
+do.call("data.table", lapply(TAB$ID[-1], function(x)
+Table(getGEO(x, getGPL = FALSE))[, -1]))
+gmSet <- data.table(IlmnIDTable[, -1], mysamples)
+} else {
+gmSet <- Table(getGEO(TAB$ID, getGPL = FALSE))
+}
+out <- GenomicRatioSet(gr = gmset, Beta = exprs(gset)[ind1,
+, drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
+annotation = c(array = array, annotation = annotation),
+preprocessMethod = preprocessing)
+out <- GenomicRatioSet(gr = gmSet, Beta = exprs(gset)[ind1,
+, drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
+annotation = c(array = array, annotation = annotation),
+preprocessMethod = preprocessing)
+??GenomicRatioSet
+sampleNames(gset)
+common
+class(gset)
+??GenomicRatioSet
+GenomicRatioSet
+getGenomicRatioSetFromGEO
+GSE <- "GSE51547"
+function (GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k",
+annotation = .default.450k.annotation, what = c("Beta", "M"),
+mergeManifest = FALSE, i = 1)
+{
+what <- match.arg(what)
+if (is.null(GSE) && is.null(path))
+stop("Either GSE or path must be supplied.")
+if (!is.null(GSE))
+gset <- GEOquery::getGEO(GSE)
+else gset <- GEOquery::getGEO(filename = file.path(path,
+list.files(path, pattern = ".soft")))
+if (length(gset) == 0)
+stop("Empty list retrieved from GEO.")
+if (length(gset) > 1) {
+warning("More than one ExpressionSet found:\n", names(gset),
+"\nUsing entry ", i)
+gset <- gset[[i]]
+}
+else gset <- gset[[1]]
+platform <- annotation(gset)
+if (platform != "GPL13534")
+warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.",
+platform))
+if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <
+0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1))
+warning("Values outside [0,1] detected. 'what' argument should not be Beta.")
+ann <- .getAnnotationString(c(array = array, annotation = annotation))
+if (!require(ann, character.only = TRUE))
+stop(sprintf("cannot load annotation package %s", ann))
+object <- get(ann)
+gr <- getLocations(object, mergeManifest = mergeManifest,
+orderByLocation = TRUE)
+locusNames <- names(gr)
+sampleNames(gset) <- gset$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
+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]]
+}
+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)$Name)
+ind2 <- match(common, locusNames)
+preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details"))
+if (what == "Beta") {
+out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1,
+, drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
+annotation = c(array = array, annotation = annotation),
+preprocessMethod = preprocessing)
+}
+else {
+out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL,
+M = exprs(gset)[ind1, , drop = FALSE], CN = NULL,
+pData = pData(gset), annotation = c(array = array,
+annotation = annotation), preprocessMethod = preprocessing)
+}
+return(out)
+}
+function (GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k",
+annotation = .default.450k.annotation, what = c("Beta", "M"),
+mergeManifest = FALSE, i = 1)
+{
+what <- match.arg(what)
+if (is.null(GSE) && is.null(path))
+stop("Either GSE or path must be supplied.")
+if (!is.null(GSE))
+gset <- GEOquery::getGEO(GSE)
+else gset <- GEOquery::getGEO(filename = file.path(path,
+list.files(path, pattern = ".soft")))
+if (length(gset) == 0)
+stop("Empty list retrieved from GEO.")
+if (length(gset) > 1) {
+warning("More than one ExpressionSet found:\n", names(gset),
+"\nUsing entry ", i)
+gset <- gset[[i]]
+}
+else gset <- gset[[1]]
+platform <- annotation(gset)
+if (platform != "GPL13534")
+warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.",
+platform))
+if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <
+0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1))
+warning("Values outside [0,1] detected. 'what' argument should not be Beta.")
+ann <- .getAnnotationString(c(array = array, annotation = annotation))
+if (!require(ann, character.only = TRUE))
+stop(sprintf("cannot load annotation package %s", ann))
+object <- get(ann)
+gr <- getLocations(object, mergeManifest = mergeManifest,
+orderByLocation = TRUE)
+locusNames <- names(gr)
+sampleNames(gset) <- gset$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)
+}
+return(out)
+}
+what <- match.arg(what)
+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.")
+what
+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)
+ann <- .getAnnotationString(c(array = array, annotation = annotation))
+ann <- .getAnnotationString(c(array = array, annotation = annotation))
+??getLocations
+getAnnotation(gset, what = "everything", lociNames = NULL,
+orderByLocation = FALSE, dropNonMapping = FALSE)
+ann <- getAnnotation(gset)
+GEODataTable
+IlmnIDTable
+matrix<- as.matrix(gmSet)
+matrix
+gr<- GRanges(matrix)
+IlmnIDTable
+GEODataTable
+getGenomicRatioSetFromGEO
+require("minfi", quietly = TRUE)
+args <- commandArgs(trailingOnly = TRUE)
+GSE = args[1]
+output = args[2]
+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)
+}
+getwd()
+GSE <- "GSE51547"
+output <- ("out.Rdata")
+require("BiocGenerics", quietly = TRUE)
+require("data.table", quietly = TRUE)
+require("GEOquery", quietly = TRUE)
+require("rtracklayer", quietly = TRUE)
+require("FDb.InfiniumMethylation.hg19", quietly = TRUE)
+require("minfi", quietly = TRUE)
+GSE <- "GSE51547"
+output <- ("out.Rdata")
+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)
+}
+out
+what
+function (GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k",
+annotation = .default.450k.annotation, what = c("Beta", "M"),
+mergeManifest = FALSE, i = 1)
+what <- match.arg(what)
+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]]
+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)}
+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]]}
+gset
+else gset <- gset[[1]]
+gset <- gset[[1]]
+gset
+gset <- gset[[i]]}
+gset <- getGEO(GSE)
+1gset <- gset[[i]]
+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)
+1gset <- gset[[i]]
+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)
+1gset <- gset[[i]]
+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]]
+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]]}
+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]]}
+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]]}}
+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
+class(gset)
+ann <- .getAnnotationString(c(array = array, annotation = annotation))
+.getAnnotationString
+getAnnotationString
+??annotation
+ann <- .getAnnotationString(c(array = array, annotation = annotation))
+if (!require(ann, character.only = TRUE))
+stop(sprintf("cannot load annotation package %s", ann))
+object <- get(ann)