downloadGEO {RCPA}

Download GEO data

Description

This function download and process data from GEO for microarray and RNASeq data.

Usage

downloadGEO(GEOID, protocol = c("affymetrix", "agilent"), platform, destDir)

Arguments

GEOID

The ID of the GEO dataset.

protocol

The protocol of selected GEO dataset.

platform

The platform of selected GEO dataset.

destDir

A path to save downloaded data. If the directory does not exist, it will be created.

Value

A vector of file paths to the downloaded files. The first element is the metadata file.

Examples

library(RCPA)
# Affymetrix
downloadPath <- file.path(tempdir(), "GSE59761")
fileList <- RCPA::downloadGEO(GEOID = "GSE59761", protocol = "affymetrix",
                                platform ="GPL16311", destDir = downloadPath)