geoConvert: Cross-reference between GEO data types

In zhujack/GEOmetadb: A compilation of metadata from NCBI GEO

Cross-reference between GEO data types

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

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 <[e-mail]>

Examples

## Use the demo GEOmetadb database:
if( !file.exists("GEOmetadb.sqlite") ) {
    demo_sqlfile <- getSQLiteFile(destdir = getwd(), destfile = "GEOmetadb.sqlite.gz", type = "demo")
} else {
    demo_sqlfile <- "GEOmetadb.sqlite"
}
ls = geoConvert('GPL96', out_type=c("GSE", 'GSM'), sqlite_db_name=demo_sqlfile)
names(ls)
head(ls[[1]])

## Download the full GEOmetadb database:
## Not run: geometadbfile <- getSQLiteFile()

zhujack/GEOmetadb documentation built on Oct. 26, 2022, 7:32 a.m.