dl_geo_processed: Download processed data from GEO for a GSE accession number

In russHyde/miiq: Microarrays Are Awesome: Get Them Analysed HERE!

Description

Given a GSE accession number (GSE12345), this function downloads the processed dataset from the Gene Expression Omnibus as a matrix. Processed data are stored as dest_dir/<gse_acc>_series_matrix.txt.gz and any annotation data is stored in dest_dir/.

Usage

dl_geo_processed(acc, dest_dir = file.path("data", "ext", "GEOquery"))

Arguments

acc	A single GSE accession number of the form "GSE12345".
dest_dir	An existing directory. The function dies if this directory is missing. Data related to gse-id are stored either in this directory (the processed data matrix and the annotation data) or in a subdirectory <gse.id> of this directory (for the raw data).

Value

A list giving the directories and filenames for all downloaded files. The list contains some entries that are only relevant to array-express downloads, rather than GEO downloads.

russHyde/miiq documentation built on Dec. 25, 2019, 10:56 a.m.