Mercurial > repos > testtool > find_dmr
view findDMR/.Rhistory @ 11:24ac6f93cc3e draft
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author | testtool |
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date | Thu, 11 May 2017 11:26:02 -0400 |
parents | 7df2b7d79391 |
children | 083895dbc289 |
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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