GSEinDB: Retrieve information about a GSE loaded in the compendium...

In compendiumdb: Tools for Retrieval and Storage of Functional Genomics Data

Description

Retrieve information about GEO series (GSE) records present in the compendium database

Usage

GSEinDB(con, GSEid = NULL)

Arguments

con	list containing a connection object specifying the user name and password to connect or interact with the compendium database (see connectDatabase)
GSEid	character vector specifying the GSE ID(s). The default value is NULL, in which case the function returns an overview of all GSEs present in the compendium database.

Value

An object of class data.frame consisting of ten columns: i) ID of the record in the compendium database, ii) GSE ID, iii) educated guess on the experimental design of the experiment, iv) GPL ID, v) number of samples, vi) user-specified tag for the experiment, (see tagExperiment), vii) NCBI taxonomy ID, viii) corresponding organism name, ix) GDS ID and x) date and time on which the data was loaded in the database

Note

The value for the variable experimentDesign is determined by parsing the sample information provided by GEO. The variable can take the following values: i) SC: single-channel design, ii) DC: double-channel design, iii) DS: double-channel dye-swap design (if the same source name occurs in both channels) and iv) CR: double-channel common reference design (if the source name is equal for all samples in one of the two channels). The attribution of 'DS' and 'CR' labels makes assumptions on how source names are represented in GEO and should be interpreted with caution.

Author(s)

Umesh K. Nandal

See Also

GDSforGSE, GSEforGPL, tagExperiment

Examples

 ## Not run: 
  conn <- connectDatabase(user="usrname",password="passwd",dbname="compendium")
  GSEinDB(conn,"GSE1657")
 
## End(Not run)

compendiumdb documentation built on May 2, 2019, 4:06 p.m.