downloadGEO: Download GEO data
In RCPA: Consensus Pathway Analysis

downloadGEO

R Documentation

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)

RCPA documentation built on May 29, 2024, 4:24 a.m.