################################################### ### chunk number 1: chunk1 ################################################### #line 287 "vignettes/ENVISIONQuery/inst/doc/ENVISIONQuery.Rnw" library(ENVISIONQuery); #check available services getServiceNames(); #check available tools for a given service service<-getService("ID Conversion"); getToolNames(service); #check available input type for a given tool service<-getService("Reactome"); tool<-getTool(service,"FindPathAdv"); getInputTypes(tool); #getAvailable options for a given service getServiceOptions("Picr"); ################################################### ### chunk number 2: chunk2 ################################################### #line 310 "vignettes/ENVISIONQuery/inst/doc/ENVISIONQuery.Rnw" #convert the Affy probeset IDs to Uniprot IDs res<-ENVISIONQuery(ids=c("1553619_a_at","1552276_a_at","202795_x_at"), serviceName="ID Conversion",toolName="Affy2Uniprot",typeName="Affymetrix ID"); print(res); #retrieve the pathways for given Uniprot ID(s) res<-ENVISIONQuery(ids="P38398",serviceName="Reactome",typeName="Uniprot ID"); print(res[1:5,]); #retrieve protein-protein interactions res<-ENVISIONQuery(ids="P38398",serviceName="Intact",typeName="Uniprot ID"); print(res[1:5,]); #convert EnSembl IDs to Uniprot IDs res<-ENVISIONQuery(ids=c("ENSP00000397145","ENSP00000269554"), serviceName="Picr",typeName="Protein ID"); print(res); ################################################### ### chunk number 3: chunk3 ################################################### #line 342 "vignettes/ENVISIONQuery/inst/doc/ENVISIONQuery.Rnw" #match Uniprot IDs to EnSembl and TrEMBL options<-list("enfin-picr-search-database"=c("ENSEMBL_HUMAN","TREMBL")); res<-ENVISIONQuery(ids="P38398",options=options, serviceName="Picr",typeName="Protein ID"); print(res); #retrieve the pathways for given Uniprot ID(s)sorting them by coverage #and calculating the total protein count options<-list("enfin-reactome-add-coverage"="true", "enfin-reactome-sort-by-coverage"="true"); res<-ENVISIONQuery(ids="P38398",options=options, serviceName="Reactome",typeName="Uniprot ID"); print(res[1:5,]); #convert the Affy probeset IDs to UniProt IDs restricting #output by micro array type and organism species filter<-list(Microarray.Platform="affy_hg_u133_plus_2", organism.species="Homo sapiens"); res<-ENVISIONQuery(ids=c("1553619_a_at","1552276_a_at","202795_x_at"), filter=filter, serviceName="ID Conversion", toolName="Affy2Uniprot",typeName="Affymetrix ID"); print(res); ################################################### ### chunk number 4: chunk4 ################################################### #line 377 "vignettes/ENVISIONQuery/inst/doc/ENVISIONQuery.Rnw" #Intact-Reactome cascaded request for UniProt ID(s). IntactReactomeXML<-ENVISIONQuery(ids="P38398", serviceName=c("Intact","Reactome"),typeName="Uniprot ID",verbose=TRUE); #convert xml text into XMLDocument #using XML package for further exploring xmlDoc<-xmlTreeParse(IntactReactomeXML,useInternalNodes = TRUE, asText=TRUE); class(xmlDoc); ################################################### ### chunk number 5: chunk5 eval=FALSE ################################################### ## #line 396 "vignettes/ENVISIONQuery/inst/doc/ENVISIONQuery.Rnw" ## filter<-list(Microarray.Platform="affy_hg_u133_plus_2", ## organism.species="Homo sapiens"); ## res<-ENVISIONQuery(ids=c("1553619_a_at","1552276_a_at","202795_x_at"), ## filter=filter, serviceName="menu",toolName="menu",typeName="menu"); ## print(res); ################################################### ### chunk number 6: sessionInfo ################################################### #line 429 "vignettes/ENVISIONQuery/inst/doc/ENVISIONQuery.Rnw" toLatex(sessionInfo())