parseGEO {GEOquery} | R Documentation

## Parse GEO text

### Description

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)

### 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.

### 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.

### Author(s)

Sean Davis

### See Also

`getGEO`

[Package GEOquery version 2.62.2 Index]