celsius {celsius} | R Documentation |
Retrieve Affymetrix microarray measurements and metadata from Celsius web services, see http://genome.ucla.edu/projects/celsius.
Package: | celsius |
Type: | Package |
Version: | 1.0.7 |
Date: | 2007-05-21 |
License: | Artistic License |
This library is intended to provide a set of accessor methods to a celsius style database. To use any of these functions, you must 1st create a Celsius Server object that points to an appropriate instance of a Celsius Database. The default parameters point to the initial instance.
Once this is created, there are a host of usable functions which can be called as needed Here is a brief overview:
getPlatformData(): returns all affy platforms supported by the server
listSamplesForPlatform(): lists all Sample IDs for a particular platform
mapIdToCelsius(): this maps foreign Sample IDs to the Celsius Server instance
getSampleData(): Returns data based on Sample IDs
getFeatureData(): Returns data based on features (affy probeset IDs)
getAssayData(): Returns an intersection of data for a set of both features and sample IDs
getCvterms(): returns information (such as ID) about available controlled vocabulary terms
getOntologyData(): Returns phenotypic data based on list of controlled voculary term IDs
getPhenoData(): returns an intersection of data for controlled vocabulary terms and specific Sample IDs
makeExprSet(): makes an expression set object from supplied IDs, features and/or controlled vocabulary terms
Allen Day and Marc Carlson Maintainer: Marc Carlson <mcarlson@fhcrc.org>
There is also individual documentation for the major functions listed above.
#first make an instance of a celsius Server object. celsius = new( "celsiusServer", celsiusUrl = "http://celsius.genomics.ctrl.ucla.edu" ); #list all of the platforms supported by the server platformTable = getPlatformData( celsius ); #list all the samples in the server that correspond to the #HG-U133_Plus_2 platform... celsius@platform = "HG-U133_Plus_2"; idList = listSamplesForPlatform( celsius ); #map some foreign IDs to the celsius servers internal sample IDs celsius@platform = 'HG-U133A'; id = c( "AEX:E-MEXP-402", "GSE6210" ); mapTable = mapIdToCelsius( celsius, id = id ); #get some samples data based on sample IDs celsius@verbose = TRUE; data = getSampleData( celsius, id = c( "SN:1005595" ) ); #get some data based on features (affymetrix probesets). data = getFeatureData( celsius, feature = c( "204412_s_at", "1316_at" ) ); #get some data that corresponds to both a set of Sample IDs AND some #features (affymetrix probesets) celsius@verbose = FALSE; data = getAssayData( celsius, id = c( "SN:1018351", "SN:1043233" ), feature = c( "201820_at", "202222_s_at", "202508_s_at", "203296_s_at" ) ); #get some information about controlled vocabulary terms #(ID is probably most important here) lungTerms = getCvterms( celsius, q = "lung", db = "MA" ); #get data on all samples (on one platform) for a particular controlled #vocabulary term data = getOntologyData( celsius, cvterm=c( "MA:0000415" ) ); #get data on all samples (on one platform) for a controlled vocabulary #term on specific samples data = getPhenoData( celsius, id = c( "SN:1000019", "SN:1000170", "SN:1005039", "SN:1004962" ), cvterm = c( "MA:0000415" ) ); #finally, we can make an expression set object straight from the #database using IDs and controlled vocabulary terms exprSet = makeExprSet( celsius, id = c( "SN:1000019", "SN:1000170", "SN:1005039" ), cvterm = c( "MA:0000415" ), feature = c( "201820_at", "202222_s_at", "202508_s_at", "203296_s_at" ) ); #Or you can also make an expression set using a foreign ID: celsius@platform = "Mouse430_2"; exprSet = makeExprSet(celsius, id = c( "GSE6210" ), cvterm = c( "MA:0000415" ), feature = c( "1415670_at", "1430537_at" ), mapids = TRUE ); #Finally, you can get raw annotations for an expression set by using the #annotations parameter celsius@platform = 'HG-U133A'; exprSet = makeExprSet( celsius, id = c( "SN:1000019", "SN:1000170", "SN:1005039" ), cvterm = c( "MA:0000415" ), feature = c( "201820_at", "202222_s_at", "202508_s_at", "203296_s_at" ), annotations = TRUE );