Nothing
path <- system.file("testScripts/R", package="aroma.affymetrix")
pathname <- file.path(path, "downloadUtils.R")
source(pathname)
verbose && enter(verbose, "Downloading raw data")
##########################################################################
# Data set:
# GSE24546,testset/
# Hs_PromPR_v02/
# GSM605951.CEL (Prec1_MeDNA_Input1)
# GSM605952.CEL (Prec1_MeDNA_IP2)
# GSM605953.CEL (Prec1_MeDNA_IP1)
#
# # Validation files (from the aroma project)
# Prec1_MeDNA_600_IP1-Input.tsv
# Prec1_MeDNA_600_IP1-Input.bar.txt
# Prec1_MeDNA_800_IPs-Input.bar.txt
#
# Overall design:
# Comparison of MeDIP/MBD for DNA methylation profiling, comparison of
# whole genome amplification techniques, using tiling array for copy
# number aberration detection and comparisons of tiling array data to
# sequencing readouts.
#
# URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24546
##########################################################################
dataSet <- "GSE24546"
tags <- "testset"
chipType <- "Hs_PromPR_v02"
sampleNamesMap <- c(
GSM605951="Prec1_MeDNA_Input1",
GSM605952="Prec1_MeDNA_IP2",
GSM605953="Prec1_MeDNA_IP1"
)
verbose && cat(verbose, "Data set: ", dataSet)
ds <- downloadGeoRawDataFiles(dataSet, tags=tags, chipType=chipType, sampleNames=names(sampleNamesMap))
print(ds)
## AffymetrixCelSet:
## Name: GSE24546
## Tags: testset
## Path: rawData/GSE24546,testset/Hs_PromPR_v02
## Platform: Affymetrix
## Chip type: Hs_PromPR_v02
## Number of arrays: 3
## Names: GSM605951, GSM605952, GSM605953 [3]
## Time period: 2007-09-28 13:17:49 -- 2007-09-28 14:26:51
## Total file size: 134.54MB
## RAM: 0.01MB
# Download MAT validation files
path <- getPath(ds)
filenames <- c("Prec1_MeDNA_600_IP1-Input.tsv", "Prec1_MeDNA_600_IP1-Input.bar.txt", "Prec1_MeDNA_800_IPs-Input.bar.txt")
pathnames <- file.path(path, filenames)
missing <- !sapply(pathnames, FUN=isFile)
if (any(missing)) {
filenames <- filenames[missing]
filenamesGZ <- sprintf("%s.gz",filenames)
urlRoot <- "https://aroma-project.org/data"
urlPath <- file.path(urlRoot, "rawData", getFullName(ds), chipType)
urls <- file.path(urlPath, filenamesGZ)
pathnamesD <- sapply(urls, FUN=function(url) {
pathnameGZ <- downloadFile(url, path=path)
gunzip(pathnameGZ)
gsub("[.]gz$", "", pathnameGZ)
})
}
verbose && exit(verbose)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.