updatePhenoData: Update the phenotypic data of a GSE record

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

Description

Update the phenotypic data of a GEO series (GSE) record and store the updated phenotypic data into the compendium database

Usage

updatePhenoData(con, GSEid, data)

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
data	character matrix object containing all GSM IDs for the GSE specified by GSEid as rownames followed by columns containing updated annotation of the corresponding samples. Column names may different from those returned by GMSdescriptions. This will overwrite the phenotypic data currently stored in the compendium database and the user is prompted to confirm this.

Author(s)

Umesh K. Nandal

Examples

 ## Not run: 
  conn <- connectDatabase(user="usrname",password="passwd",dbname="compendium")
  
  GSMdescriptions(conn,"GSE18290")
  tab <- GSMdescriptions(conn,"GSE18290")

  # As an example just replace the current annotation by the same annotation
  updatePhenoData(conn,"GSE18290",tab)
  GSMdescriptions(conn,"GSE18290")

 
## End(Not run)

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