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,
  platform,
  protocol = c("affymetrix", "agilent"),
  destDir,
  greenOnly = TRUE
)

Arguments

`GEOID`	The ID of the GEO dataset.
`platform`	The platform of selected GEO dataset.
`protocol`	The protocol of the selected GEO dataset, including affymetrix and agilent.
`destDir`	A path to save downloaded data.
`greenOnly`	Logical, for use with source, should the green (Cy3) channel only be read, or are both red and green required.

Value

A SummarizedExperiment object including the following attributes:

assay: The assay data matrix, where rows are genes and columns are samples
colData: The data frame of sample information

Examples


library(RCPA)
# Affymetrix
downloadPath <- file.path(tempdir(), "GSE59761")
if(!dir.exists(downloadPath)) dir.create(downloadPath)
affyDataset <- RCPA::downloadGEO(GEOID = "GSE59761", platform ="GPL16311",
                                 protocol ="affymetrix", destDir = downloadPath)

RCPA documentation built on Nov. 21, 2023, 5:08 p.m.