getAssayData {celsius}R Documentation

Get Celsius data using IDs, probesets OR the intersection of data that corresponds to BOTH IDs and probesets.

Description

This function is to intelligently get the data from the DB so that the data is retrieved in the fastest possible way. IF only IDs are given, then it will only return the full data on THOSE, if only an feature list is given, then it will return ALL the data for that platform on only those elements, and finally, if both a ID and an feature list are given then it will decide whether to retrieve on IDs and restrict by elements, or vice versa (just depending on what is faster).

Usage

getAssayData( celsiusObject, id = NULL, feature = NULL );

Arguments

celsiusObject Provide a celsius server object with approriate URLs
id character vector of IDs, database accession identifiers for CEL records used in Celsius
feature character vector of feature IDs, database accession identifiers for probeset records used in Celsius

Value

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

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 = getAssayData( celsius,
  id = c( "SN:1018351" ),
  feature = c( "201820_at", "202222_s_at", "202508_s_at", "203296_s_at",
  "203400_s_at" ) );

data = getAssayData( celsius,
  id = c( "SN:1018351", "SN:1043233" ),
  feature = c( "201820_at" ) );

data = getAssayData( celsius,
  id = c( "SN:1018351", "SN:1043233" ) );

data = getAssayData( celsius,
  feature = c( "201820_at", "202222_s_at" ) );

data = getAssayData( celsius,
  id = c( "SN:1018351", "SN:1043233" ),
  feature = c( "201820_at", "202222_s_at", "202508_s_at", "203296_s_at",
  "203400_s_at" ) );

data = getAssayData( celsius,
  id = c( "SN:1018351", "SN:1043233", "SN:1018331", "SN:1041970",
  "SN:1008042" ),
  feature = c( "201820_at","202222_s_at" ));

data = getAssayData( celsius,
  id = c( "SN:1018351" ),
  feature = c( "201820_at" ) );

[Package celsius version 1.0.7 Index]