Download a file from GEO soft file to the local machine

This function simply downloads a SOFT format file associated with the GEO accession number given.

Usage

getGEOfile(
  GEO,
  destdir = tempdir(),
  AnnotGPL = FALSE,
  amount = c("full", "brief", "quick", "data")
)

Arguments

GEO: Character string, the GEO accession for download (eg., GDS84, GPL96, GSE2553, or GSM10)
destdir: Directory in which to store the resulting downloaded file. Defaults to tempdir()
AnnotGPL: A boolean defaulting to FALSE as to whether or not to use the Annotation GPL information. These files are nice to use because they contain up-to-date information remapped from Entrez Gene on a regular basis. However, they do not exist for all GPLs; in general, they are only available for GPLs referenced by a GDS
amount: Amount of information to pull from GEO. Only applies to GSE, GPL, or GSM. See details...

Value

Invisibly returns the full path of the downloaded file.

Details

This function downloads GEO SOFT files based on accession number. It does not do any parsing. The first two arguments should be fairly self-explanatory, but the last is based on the input to the acc.cgi url at the geo website. In the default 'full' mode, the entire SOFT format file is downloaded. Both 'brief' and 'quick' offer shortened versions of the files, good for 'peeking' at the file before a big download on a slow connection. Finally, 'data' downloads only the data table part of the SOFT file and is good for downloading a simple EXCEL-like file for use with other programs (a convenience).

References

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi

Author

Sean Davis

Examples


# myfile <- getGEOfile('GDS10')