changeset 65:ad054b925eda draft

Uploaded

--- a/GRsetFromGEO/.Rhistory	Fri Apr 28 11:12:27 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-require("minfi", quietly = TRUE)
-?require
-require("minfi", quietly = TRUE)
-minfi
-as.data.frame(GRset)
-GRset <- getGenomicRatioSetFromGEO(GSE)
-getGenomicRatioSetFromGEO

Binary file GRsetFromGEO/._.DS_Store has changed

--- a/GRsetFromGEO/GRsetFromGEO.R	Fri Apr 28 11:12:27 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-require("minfi", quietly = TRUE)
-
-options(warn = -1)
-options("download.file.method"="wget")
-
-args <- commandArgs(trailingOnly = TRUE)
-GSE = args[1] 
-output = args[2] 
-
-GRset <- getGenomicRatioSetFromGEO(GSE)
-
-save(GRset,file = output)

--- a/GRsetFromGEO/GRsetFromGEO.xml	Fri Apr 28 11:12:27 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool id="GetGEO" name="GRsetFromGEO" version="1.16.2">
-  <description>
-    Reading Illumina methylation array data from GEO
-  </description>
-  <macros>
-      <import>GRsetFromGEO_macros.xml</import>
-  </macros>
-      <expand macro="requirements" />
-<stdio>
-   <exit_code range="1:" />
-</stdio>
-  <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command>
-  <inputs>
-     <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
-  </inputs>
-  <outputs>
-    <data format="RDdata" name="output" label="GRsetFromGEO.RData"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="test">
-      <element name="test-data">
-          <collection type="data">
-                <element name="GSE" value="GSE51547"/>
-          </collection>
-        </element>
-        </param>
-        <output type="data" format="RData"  name="output" label="test-data/out.RData"/>
-        </test>
-    </tests>
-  <help>
-**Description**
-</help>
-<citations>
-GEO
-</citations>
-</tool>

--- a/GRsetFromGEO/GRsetFromGEO_macros.xml	Fri Apr 28 11:12:27 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-<macros>
-    <xml name="requirements">
-        <requirements>
-	  	    <requirement type="package" version="3.2.1">R</requirement>
-	         <requirement type="package" version="0.0.1">dependency</requirement>
-        </requirements>
-    </xml>
-	<xml name="citations">
-	    <citations>
-		    <citation type="doi">10.1093/bioinformatics/btu049</citation>
-        </citations>
-    </xml>
-</macros>

Binary file GRsetFromGEO/test-data/._.DS_Store has changed

Binary file GRsetFromGEO/test-data/out.RData has changed

--- a/GRsetFromGEO/tool_dependencies.xml	Fri Apr 28 11:12:27 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="dependency" version="0.0.1">
-      # TODO:
-        <repository changeset_revision="ebffd425f521" name="450kdependency" owner="testtool" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="R" version="3.2.1">
-        <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getGEO/.Rhistory	Thu May 11 06:31:45 2017 -0400
@@ -0,0 +1,7 @@
+??options
+options(warn = -1)
++options("download.file.method"="wget")
+options("download.file.method"="wget")
+options(warn = -1,"download.file.method"="wget")
+??getPlatform
+??getPlatform

Binary file getGEO/._.DS_Store has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getGEO/getGEO.R	Thu May 11 06:31:45 2017 -0400
@@ -0,0 +1,54 @@
+require("BiocGenerics", quietly = TRUE)
+require("data.table", quietly = TRUE)
+require("GEOquery", quietly = TRUE)
+require("rtracklayer", quietly = TRUE)
+require("FDb.InfiniumMethylation.hg19", quietly = TRUE)
+
+options("download.file.method.GEOquery"="wget")
+options(warn = -1)
+
+args <- commandArgs(trailingOnly = TRUE)
+GSMTable = args[1]
+protocol = args[2]
+platform = args[3]
+Data_Table = args[4]
+
+TAB = fread(GSMTable)
+
+if (is.null(TAB)) {
+  stop("Must specify input files")
+} else {
+  GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE)
+  IlmnIDTable <- Table(GEODataTable)
+  MetaData <- data.frame(Meta(GEODataTable))
+
+
+  write.table(MetaData, protocol, row.names = FALSE, sep = "\t")
+}
+
+hm450.hg19 <- getPlatform()
+
+IlmnInfo <-
+  data.table(
+    IlmnID = names(hm450.hg19),
+    CHR = as.data.frame(hm450.hg19@seqnames)$value,
+    BP = as.numeric(hm450.hg19@elementMetadata$probeStart)
+  )
+
+
+write.table(IlmnInfo, platform, row.names = FALSE, sep = "\t")
+
+
+if (length(TAB$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))
+}
+
+write.table(gmSet, Data_Table, row.names = FALSE,quote=FALSE,sep="\t")
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getGEO/getGEO.xml	Thu May 11 06:31:45 2017 -0400
@@ -0,0 +1,40 @@
+<tool id="GEO" name="getGEO" version="1.16.2">
+  <requirements>
+        <requirement type= "package" version="0.0.1">450kdependency</requirement>
+         <requirement type="package" version="3.2.1">R</requirement>
+     </requirements>
+<stdio>
+    <exit_code range="1:" />
+ </stdio>
+  <command> Rscript $__tool_directory__/getGEO.R "$GSMTable" "$protocol" "$platform" "$Data_Table"</command>
+  <inputs>
+    <param optional="false" format="txt" name="GSMTable" type="data" value="" help="GEO table of data." label="[required] GSMTable">
+      <validator type="empty_field" message="This field is required."/>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="txt" name="protocol" label="protocol.txt"/>
+    <data format="txt" name="platform" label="platform.txt"/>
+    <data format="txt" name="Data_Table" label="Data_Table.txt"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="test">
+      <element name="test-data">
+          <collection type="data">
+              <element name="GSMTable" value="test-data/input.txt" />
+          </collection>
+        </element>
+        </param>
+        <output format="txt" name="protocol" label="test-data/protocol.txt"/>
+        <output format="txt" name="platform" label="test-data/platform.txt"/>
+        <output format="txt" name="Data_Table" label="test-data/Data_Table.txt"/>
+        </test>
+    </tests>
+  <help>
+**Description**
+</help>
+<citations>
+GEO
+</citations>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getGEO/test-data/.Rhistory	Thu May 11 06:31:45 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)

Binary file getGEO/test-data/._.DS_Store has changed

Binary file getGEO/test-data/._input.csv has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getGEO/test-data/IlmnTable.txt	Thu May 11 06:31:45 2017 -0400
@@ -0,0 +1,485578 @@
+"IlmnID","CHR","BP"
+"cg04913815","chr16",60438
+"cg01686861","chr16",60700
+"cg05558259","chr16",61037
+"cg26978960","chr16",62412
+"cg03792876","chr16",73195
+"cg09699726","chr16",91554
+"cg07549526","chr16",91663
+"cg02851049","chr16",101212
+"cg11876012","chr16",101638
+"cg14820573","chr16",102073
+"cg14747225","chr16",102976
+"cg16670573","chr16",103375
+"cg09499248","chr16",103483
+"cg00762468","chr16",103568
+"cg05055400","chr16",103592
+"cg09969830","chr16",103646
+"cg00958578","chr16",103715
+"cg11653271","chr16",103723
+"cg01188584","chr16",103853
+"cg03974483","chr16",103985
+"cg08718695","chr16",104135
+"cg01062126","chr16",104539
+"cg00992207","chr16",107404
+"cg00914902","chr16",108066
+"cg27248189","chr16",110257
+"cg06194960","chr16",111362
+"cg07608562","chr16",111610
+"cg20220196","chr16",111753
+"cg09201525","chr16",111823
+"cg03333116","chr16",112396
+"cg04721268","chr16",112802
+"cg01403103","chr16",112804
+"cg01502407","chr16",113107
+"cg04322210","chr16",114987
+"cg26933686","chr16",115957
+"cg00179196","chr16",117934
+"cg07405083","chr16",119384
+"cg06934747","chr16",120902
+"cg00525011","chr16",122031
+"cg03948744","chr16",122515
+"cg00079891","chr16",122716
+"cg09113560","chr16",122764
+"cg04995976","chr16",123198
+"cg06230303","chr16",123353
+"cg01262217","chr16",123363
+"cg04260507","chr16",123553
+"cg17199481","chr16",123676
+"cg01422009","chr16",125896
+"cg03462322","chr16",126397
+"cg16383109","chr16",126403
+"cg03110993","chr16",126800
+"cg03492469","chr16",126855
+"cg05501742","chr16",126844
+"cg16003913","chr16",127072
+"cg04257263","chr16",127088
+"cg15017278","chr16",127401
+"cg02729269","chr16",127772
+"cg07395378","chr16",127904
+"cg01609171","chr16",127949
+"cg10009236","chr16",127968
+"cg05397937","chr16",128446
+"cg15768556","chr16",128630
+"cg05394456","chr16",129230
+"cg10143220","chr16",129454
+"cg00935108","chr16",129562
+"cg02949481","chr16",131514
+"cg05791870","chr16",136656
+"cg07484220","chr16",136761
+"cg07405534","chr16",139691
+"cg26925590","chr16",139704
+"cg07371452","chr16",139732
+"cg04807152","chr16",147558
+"cg16730559","chr16",157323
+"cg02353723","chr16",163133
+"cg09430181","chr16",175615
+"cg02028423","chr16",185078
+"cg01527023","chr16",188138
+"cg00928894","chr16",188221
+"cg02369618","chr16",188603
+"cg09580244","chr16",188684
+"cg02783232","chr16",188741
+"cg08524197","chr16",188802
+"cg02855078","chr16",188815
+"cg08969593","chr16",188855
+"cg06171619","chr16",188884
+"cg00389577","chr16",189052
+"cg24399405","chr16",189577
+"cg27009501","chr16",192791
+"cg06929449","chr16",199366
+"cg10317591","chr16",199773
+"cg08957279","chr16",202263
+"cg10164238","chr16",202320
+"cg21960110","chr16",202434
+"cg01839639","chr16",202542
+"cg25425005","chr16",202905
+"cg07263153","chr16",202926
+"cg08400316","chr16",204221
+"cg02279719","chr16",204474
+"cg06459847","chr16",204601
+"cg07498624","chr16",204783
+"cg01923692","chr16",204949
+"cg06031493","chr16",210205
+"cg05390075","chr16",210528
+"cg07067950","chr16",212416
+"cg07893512","chr16",214728
+"cg05057452","chr16",214922
+"cg25322095","chr16",215002
+"cg07466193","chr16",215362
+"cg01744019","chr16",215545
+"cg09812623","chr16",215733
+"cg08393070","chr16",215743
+"cg01558909","chr16",215797
+"cg26540367","chr16",215816
+"cg06319822","chr16",215912
+"cg26976732","chr16",216052
+"cg21664030","chr16",216244
+"cg04141813","chr16",216450
+"cg03309232","chr16",216626
+"cg12251336","chr16",216719
+"cg09523819","chr16",216709
+"cg04321267","chr16",219107
+"cg04377849","chr16",221536
+"cg26637826","chr16",221542
+"cg04938149","chr16",221811
+"cg15597257","chr16",222837
+"cg00697413","chr16",222858
+"cg16263182","chr16",223351
+"cg05956679","chr16",223360
+"cg01319583","chr16",224880
+"cg01704105","chr16",225666
+"cg08923033","chr16",226002
+"cg06235582","chr16",226668
+"cg27452732","chr16",226670
+"cg10647513","chr16",227155
+"cg09434193","chr16",227185
+"cg08923355","chr16",227469
+"cg05933901","chr16",229407
+"cg26729101","chr16",229452
+"cg05274179","chr16",229480
+"cg17714030","chr16",229935
+"cg07703401","chr16",230293
+"cg02401454","chr16",230295
+"cg00655203","chr16",230548
+"cg06861209","chr16",231149
+"cg05413988","chr16",231341
+"cg12617928","chr16",231742
+"cg16367168","chr16",231905
+"cg03788090","chr16",233014
+"cg02573966","chr16",235507
+"cg17291625","chr16",236032
+"cg02385593","chr16",237231
+"cg00126636","chr16",237282
+"cg08685832","chr16",238934
+"cg04958271","chr16",239231
+"cg06348427","chr16",239291
+"cg06950479","chr16",240114
+"cg02933542","chr16",275872
+"cg06819375","chr16",278788
+"cg01687051","chr16",278804
+"cg16767297","chr16",279223
+"cg22470426","chr16",279634
+"cg27362010","chr16",279746
+"cg26697334","chr16",279942
+"cg07080946","chr16",279998
+"cg05465347","chr16",281115
+"cg07992604","chr16",281116
+"cg22621780","chr16",281201
+"cg02877856","chr16",281236
+"cg05657096","chr16",281424
+"cg02655906","chr16",283415
+"cg26713125","chr16",284384
+"cg00594300","chr16",284396
+"cg26887465","chr16",284463
+"cg26762198","chr16",284647
+"cg08899291","chr16",284932
+"cg12197254","chr16",285110
+"cg01532600","chr16",285140
+"cg27069188","chr16",285785
+"cg26951000","chr16",288323
+"cg16658177","chr16",299453
+"cg27316939","chr16",302804
+"cg02895698","chr16",303117
+"cg05849772","chr16",303182
+"cg03991592","chr16",303144
+"cg10293297","chr16",304556
+"cg01560407","chr16",310489
+"cg01103443","chr16",310543
+"cg06507072","chr16",310683
+"cg08694735","chr16",311131
+"cg09614814","chr16",311101
+"cg27277974","chr16",312388
+"cg07628300","chr16",312565
+"cg26484247","chr16",313377
+"cg09275921","chr16",313711
+"cg16382722","chr16",314126
+"cg08713437","chr16",314666
+"cg01854389","chr16",314779
+"cg00418913","chr16",314811
+"cg01474600","chr16",315516
+"cg05045498","chr16",318213
+"cg09192940","chr16",318646
+"cg09937849","chr16",318717
+"cg08735550","chr16",318900
+"cg02892402","chr16",320565
+"cg01127994","chr16",322725
+"cg05772319","chr16",323015
+"cg27040030","chr16",325184
+"cg02410200","chr16",325290
+"cg03390211","chr16",325826
+"cg07258794","chr16",326049
+"cg01155930","chr16",326064
+"cg07430849","chr16",326397
+"cg21946698","chr16",326567
+"cg02921617","chr16",326625
+"cg01344518","chr16",326680
+"cg26876334","chr16",329634
+"cg08199013","chr16",330010
+"cg27560922","chr16",330219
+"cg16552945","chr16",330684
+"cg15755548","chr16",331002
+"cg16447794","chr16",331207
+"cg08496521","chr16",331306
+"cg08853359","chr16",331406
+"cg08203127","chr16",331679
+"cg01309213","chr16",331773
+"cg09417849","chr16",331844
+"cg03663874","chr16",332467
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+"cg27392802","chr16",332657
+"cg09357140","chr16",332745
+"cg02428506","chr16",332777
+"cg10826763","chr16",332963
+"cg10151162","chr16",333056
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+"cg07326665","chr16",334397
+"cg00382227","chr16",334509
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+"cg08914678","chr16",334841
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+"cg08140236","chr16",337132
+"cg06233593","chr16",337645
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+"cg26462212","chr16",339496
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+"cg09548897","chr16",341277
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+"cg08134324","chr16",341964
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+"cg27480957","chr16",345406
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+"cg16412914","chr16",358200
+"cg01517185","chr16",358490
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+"cg04322644","chr16",392392
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+"cg09121920","chr16",397672
+"cg25023245","chr16",401938
+"cg08942073","chr16",402320
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+"cg15001381","chr16",403266
+"cg08577231","chr16",403800
+"cg09593385","chr16",407169
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+"cg07631681","chr16",410001
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+"cg03923285","chr16",412168
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+"cg01546397","chr16",451595
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+"cg06935581","chr16",451817
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+"cg25672287","chr16",452044
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+"cg07205857","chr16",455009
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+"cg05553342","chr16",457820
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+"cg26946311","chr16",459744
+"cg04180723","chr16",459917
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+"cg03953980","chr16",460317
+"cg27665823","chr16",460516
+"cg07969308","chr16",460698
+"cg03640864","chr16",461701
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+"cg09555736","chr16",474271
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+"cg03319323","chr16",475595
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+"cg26780138","chr16",477087
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+"cg08385995","chr16",512962
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+"cg09408143","chr16",524730
+"cg07740599","chr16",524809
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