Cross-reference between GEO data types

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Description

A common task is to find all the GEO entities of one type associated with another GEO entity (eg., find all GEO samples associated with GEO platform 'GPL96'). This function provides a very fast mapping between entity types to facilitate queries of this type.

Usage

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geoConvert(in_list, out_type = c("gse", "gpl", "gsm", "gds", "smatrix"), sqlite_db_name = "GEOmetadb.sqlite")

Arguments

in_list

Character vector of GEO entities to convert from.

out_type

Character vector of GEO entity types to which to convert.

sqlite_db_name

The filename of the GEOmetadb sqlite database file

Value

A list of data.frames.

Author(s)

Jack Zhu <zhujack@mail.nih.gov>

References

http://meltzerlab.nci.nih.gov/apps/geo, http://gbnci.abcc.ncifcrf.gov/geo/

Examples

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if(file.exists("GEOmetadb.sqlite")) {
  geoConvert('GPL96',out_type='GSM')
} else {
  print("Run getSQLiteFile() to get a copy of the GEOmetadb SQLite file
and then rerun the example")
}