getPhenoData {celsius}R Documentation

Retrieve a matrix of annotations from controlled vocabulary terms

Description

The following is a function to just retrieve a list of annotation terms ON a set list of IDs, or for all IDS (if none are provided). All Annots retrieved are specific to one platform.

Usage

getPhenoData(celsiusObject, id = NULL, cvterm = NULL);

Arguments

celsiusObject Provide a celsius server object with approriate URLs
id Provide a vector of ids
cvterm Provide a list of cvterms

Value

Return value is a table with col labels as SN identifiers and row labels as annotation terms.

Author(s)

Marc Carlson and Allen Day

Examples

#make a celsius instance
celsius = new( "celsiusServer",
  celsiusUrl = "http://celsius.genomics.ctrl.ucla.edu" );

#ways you can get the data
data = getPhenoData( celsius,
  id = c( "SN:1000019", "SN:1000170", "SN:1005039", "SN:1004962",
  "SN:1005722", "SN:1006573" ),
  cvterm = c( "MA:0000168", "MPATH:218" ) ); 

celsius@transform = TRUE;
data = getPhenoData( celsius,
  id = c( "SN:1000019", "SN:1000170", "SN:1005039", "SN:1004962",
  "SN:1005722", "SN:1006573" ),
  cvterm = c( "MA:0000168", "MPATH:218" ) );

data = getPhenoData( celsius, cvterm = c( "MA:0000168", "MPATH:218" ) );

celsius@transform = FALSE;
data = getPhenoData( celsius,
  id = c( "SN:1000019", "SN:1000170", "SN:1005039", "SN:1004962",
  "SN:1005722", "SN:1006573" ),
  cvterm = c( "MPATH:218" ) ); 

data = getPhenoData( celsius,
  id = c( "SN:1000019" ),
  cvterm = c( "MA:0000168", "MPATH:218" ) ); 

data = getPhenoData( celsius,
  id = c( "SN:1000019" ), cvterm = c( "MPATH:218" ) );

[Package celsius version 1.0.7 Index]