parseGEO: Parse GEO text

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

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

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