getGEOSuppFiles: Get Supplemental Files from GEO

In seandavi/GEOquery: Get data from NCBI Gene Expression Omnibus (GEO)

Get Supplemental Files from GEO

Description

NCBI GEO allows supplemental files to be attached to GEO Series (GSE), GEO platforms (GPL), and GEO samples (GSM). This function 'knows' how to get these files based on the GEO accession. No parsing of the downloaded files is attempted, since the file format is not generally knowable by the computer.

Usage

getGEOSuppFiles(
  GEO,
  makeDirectory = TRUE,
  baseDir = getwd(),
  fetch_files = TRUE,
  filter_regex = NULL
)

Arguments

GEO	A GEO accession number such as GPL1073 or GSM1137
makeDirectory	Should a 'subdirectory' for the downloaded files be created? Default is TRUE. If FALSE, the files will be downloaded directly into the baseDir.
baseDir	The base directory for the downloads. Default is the current working directory.
fetch_files	logical(1). If TRUE, then actually download the files. If FALSE, just return the filenames that would have been downloaded. Useful for testing and getting a list of files without actual download.
filter_regex	A character(1) regular expression that will be used to filter the filenames from GEO to limit those files that will be downloaded. This is useful to limit to, for example, bed files only.

Details

Again, just a note that the files are simply downloaded.

Value

If fetch_files=TRUE, a data frame is returned invisibly with rownames representing the full path of the resulting downloaded files and the records in the data.frame the output of file.info for each downloaded file. If fetch_files=FALSE, a data.frame of URLs and filenames is returned.

Author(s)

Sean Davis [e-mail]

Examples

a <- getGEOSuppFiles('GSM1137', fetch_files = FALSE)
a

seandavi/GEOquery documentation built on Oct. 29, 2024, 1:24 p.m.