getPhenoData {celsius} | R Documentation |
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.
getPhenoData(celsiusObject, id = NULL, cvterm = NULL);
celsiusObject |
Provide a celsius server object with approriate URLs |
id |
Provide a vector of ids |
cvterm |
Provide a list of cvterms |
Return value is a table with col labels as SN identifiers and row labels as annotation terms.
Marc Carlson and Allen Day
#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" ) );