GEOquery (version 2.38.4)

parseGEO: Parse GEO text

Description

Workhorse GEO parsers.

Usage

parseGEO(fname, GSElimits, destdir=tempdir(), AnnotGPL=FALSE, getGPL=TRUE)
parseGPL(fname)
parseGDS(fname)
parseGSE(fname, GSElimits)
parseGSM(fname)

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.

See Also

getGEO