ENVISIONQuery: Launch a query against Envision, a web online query system...
In ENVISIONQuery: Retrieval from the ENVISION bioinformatics data portal into R

Description Usage Arguments Value Note Author(s) Examples

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)