Workhorse GEO parsers.
Usage
parseGEO(
fname,
GSElimits,
destdir = tempdir(),
AnnotGPL = FALSE,
getGPL = TRUE
)Arguments
- fname
The filename of a SOFT format file. If the filename ends in .gz, a gzfile() connection is used to read the file directly.
- GSElimits
Used to limit the number of GSMs parsed into the GSE object; useful for memory management for large GSEs.
- destdir
The destination directory into which files will be saved (to be used for caching)
- AnnotGPL
Fetch the annotation GPL if available
- getGPL
Fetch the GPL associated with a GSEMatrix entity (should remain TRUE for all normal use cases)
Value
parseGEO returns an object of the associated type. For example, if it is passed the text from a GDS entry, a GDS object is returned.
Details
These are probably not useful to the end-user. Use getGEO to access these functions. parseGEO simply delegates to the appropriate specific parser. There should be no reason to use the parseGPL, parseGDS, parseGSE, or parseGSM functions directly.