Question: RDAVIDWebService - unable to use getFunctionalAnnotationChart with "count = 0"
0
14 months ago by
rdalbanus0 wrote:

Hi, all,

I'm doing TF annotations based on their protein domains using RDAVIDWebService. For some of the analyses, I want to directly compare enrichments between two groups of TFs. In order to do so, I need to get their enrichment values for all the terms in the category. One can do this by setting count = 0 and threshold = 1 in getFunctionalAnnotationChart().

Unfortunately, this does not work - the query system can't handle count = 0. Any ideas how to solve this short of going to the website and doing it manually? I have multiple gene lists, so this is essentially unfeasible.

library(RDAVIDWebService)

# Connect to DAVID (new url from https://support.bioconductor.org/p/70090/)
david_url <- "https://david.ncifcrf.gov/webservice/services/DAVIDWebService.DAVIDWebServiceHttpSoap12Endpoint/"
my_email <- "your_email@domain.edu" # Be sure to register to DAVID before doing it.
david <- DAVIDWebService\$new(email="my@email.edu", url=david_url)

# Define databases to query
query_db <- c("GENE3D", "INTERPRO", "PFAM", "PIR_SUPERFAMILY", "PRINTS",
"PRODOM", "PROSITE", "SMART", "SUPFAM", "TIGRFAMS")
setAnnotationCategories(david, query_db)

# Set gene list
some_gene_list <- c("ENSG00000139083","ENSG00000070444","ENSG00000118260","ENSG00000105967", "ENSG00000123685","ENSG00000163435","ENSG00000126456","ENSG00000168621","ENSG00000117595","ENSG00000126767")
addList(david, some_gene_list, idType = "ENSEMBL_GENE_ID", listName = "test", listType = "Gene")

# Run
getFunctionalAnnotationChart(david, threshold = 1, count = 0)


Which will crash:

Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,  :
org.apache.axis2.AxisFault: Exception occurred while trying to invoke service method getChartReport


I appreciate any input and will be happy to give more details.

rdavidwebservice david • 221 views