GSMdescriptions: List sample annotation of samples for a given GSE

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

Description

Extract the phenotypic data of each sample record (GSM) in the specified GSE in a tabular format

Usage

GSMdescriptions(con, GSEid, GPLid = "")

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 string specifying the GSE ID
GPLid	character string specifying the GPL ID. The default value is "", in which case the phenotypic data will be extracted for each of the GPLs in the GSE specified by GSEid.

Details

The function uses the corresponding GDS (if available for that GSE) in order to retrieve the phenotypic data. If a GDS is not available, it generates phenotypic data based on the sample characteristics, sample source, and sample title specified for each GSM. In case of a double-channel experiment, sample characteristics and sample source are given for both channels.

Value

A character matrix containing a row for each GSM and columns for the phenotypic data and the GPL ID(s) of the platform used.

Author(s)

Umesh K. Nandal

Examples

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

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