ENVISIONQuery {ENVISIONQuery} | R Documentation |
Launch a query against Envision, a web online query system providing elaborated information for EnCORE services. Return the results into an R object.
ENVISIONQuery(ids=c("1553619_a_at", "1553497_at"), typeName="menu", serviceName="menu", toolName="menu", chunk=1000, details=TRUE, writeHTML=FALSE, testMe=FALSE, graphicMenu=getOption("menu.graphics"), formatIt=TRUE, options=list(), filter=list(), compact=TRUE, verbose=FALSE)
ids |
Depending on input type, IDs for desired objects as a character vector a character string containing the entire Enfin xml document or a name of an Enfin xml file. |
typeName |
Type of input ids. If 'menu' (default), a menu is constructed allowing to choose one of the available types. |
serviceName |
The Envision service name or a character vector of service names. In a latter case system compbines requests into pipeline using the output of current service request as an input for a next one. If 'menu' (default), the menu is contructed allowing to choose one of the available services. |
toolName |
The tool for a particular envision service. If 'menu' (default) and there is more than one tool available, a menu is contructed allowing to choose one of the available tools. |
chunk |
The number of IDs retrieved during a single query session. In case the number of IDs exceeds the chunk size, the whole ID set is retrieved during multiple query sessions overcoming the potential limitations on a single query session ID set size. If NA, a single session is used. Default is 1000. |
details |
If TRUE (default), a list of intermediate results is returned; otherwise, just the final query result. Note: not implemented at this time |
writeHTML |
If TRUE (default is FALSE), write the received intermediate HTML to files. |
testMe |
If TRUE (default is FALSE), assign default values and run. |
graphicMenu |
If TRUE (default is FALSE), use a GUI window for the pick menus. |
formatIt |
If TRUE (default), try to interpret the returned character table and structure the result. If false, the character string representing the entire enfinXML file returned by ENVISION. Note: formatting is implemented only for 'Probe2Uniprot' and 'ID conversion' services at this time. If false, the character string representing the entire enfinXML file returned by ENVISION. |
options |
The (optional)list each element of which represents the <name,value> pair used to apply the additional constraints when sending a query to a particular service (maximum number of pathways for Reactome service as an example) |
filter |
The (optional)list where the name of each element represents the formatted output data frame column on which filetering is to be performed ('organism.species', 'Microarray.platform' etc.) and the list element containing a character vector defining the set of values on which the merging (intersection) for a given column will be performed ('Homo sapiens' for 'organism.species', 'affy_hg_u133_plus_2' for 'Microarray.platform' etc.). The filtering is performed if the list is not empty and the formatIt=TRUE. Default is an empty list. |
compact |
If TRUE and the formatted output (formatIt = TRUE)is represented by a data frame, collapses the rows with duplicated match sets but different attributes into a single row with unique match set and an attribute list separated by comma for each attribute column. Default is TRUE. |
verbose |
If TRUE (default is FALSE), more debugging information is printed. |
The ENVISIONQueryResult structure or NULL if no results were found.
For a pipeline of services, only unformatted output supported at this time.
Alex Lisovich, Roger Day
#### basic ENVISIONQuery request #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[,-3]); #retrieve protein-protein interactions res<-ENVISIONQuery(ids="P38398",serviceName="Intact",typeName="Uniprot ID"); print(res[1:5,]); #convert EnSembl IDs to Uniprot IDs try({res<-ENVISIONQuery(ids=c("ENSP00000397145","ENSP00000269554"),serviceName="Picr",typeName="Protein ID");}) print(res); #### ENVISIONQuery request using options and filters #match Uniprot IDs to EnSembl and TrEMBL options<-list("enfin-picr-search-database"=c("ENSEMBL_HUMAN","TREMBL")); try({res<-ENVISIONQuery(ids="P38398",serviceName="Picr",options=options,typeName="Protein ID");}) print(res); #retrieve the pathways for given Uniprot ID(s)sorting them by coverage #and calcultating the total protein count options<-list("enfin-reactome-add-coverage"="true", "enfin-reactome-sort-by-coverage"="true"); res<-ENVISIONQuery(ids="P38398",serviceName="Reactome",options=options,typeName="Uniprot ID"); print(res[,-3]); #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); #### pipeline of ENVISIONQuery requests. As of recent version, #### output formatting for a pipelined request is not supported yet. #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 if(!is.null(IntactReactomeXML)){ xmlDoc<-xmlTreeParse(IntactReactomeXML,useInternalNodes = TRUE, asText=TRUE); class(xmlDoc); } #### interactive ENVISIONQuery requests ## Not run: res<-ENVISIONQuery(ids=c("1553619_a_at","1552276_a_at","202795_x_at"),filter=filter, serviceName="menu",toolName="menu",typeName="menu"); print(res); ## End(Not run)