--- a/findDMR/.Rhistory	Thu May 11 11:26:02 2017 -0400
+++ b/findDMR/.Rhistory	Mon Jun 12 11:05:04 2017 -0400
@@ -1,200 +1,1 @@
-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
+??fread