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)