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This snippet illustrates how to query David from R, using the RDAVIDWebService package.
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# This snippet illustrates how to query David from R, using the RDAVIDWebService package. | |
# Load RDAVIDWebService. | |
library("RDAVIDWebService") | |
# Create a DAVIDWebService object connected to David, using your registration email. | |
# To register, go to: http://david.abcc.ncifcrf.gov/content.jsp?file=WS.html. | |
david <- DAVIDWebService$new(email='[email protected]') | |
# Define foreground and background gene lists. | |
# The foreground list should be contained within the background list. | |
FG <- addList(david, myForegroundGenes, idType="REFSEQ_MRNA", listName="isClass", listType="Gene") | |
BG <- addList(david, myBackgroundGenes, idType="REFSEQ_MRNA", listName="all", listType="Background") | |
# Inspect FG and BG to see the proportion of genes recognized by David, and those that are unmapped. | |
FG | |
BG | |
# Inspect "david" object to see the gene lists selected as foreground and background. | |
david | |
# Specifiy annotation categories. | |
setAnnotationCategories(david, c("GOTERM_BP_ALL", "GOTERM_MF_ALL", "GOTERM_CC_ALL")) | |
# Get functional annotation chart as R object. | |
FuncAnnotChart <- getFunctionalAnnotationChart(david) | |
# Print functional annotation chart to file. | |
getFunctionalAnnotationChartFile(david, "FuncAnnotChart.tsv") | |
# Get functional annotation clustering (limited to 3000 genes). | |
FuncAnnotClust <- getClusterReport(david) | |
# Print functional annotation clustering to file (limited to 3000 genes). | |
getClusterReportFile(david, "FuncAnnotClust.tsv") |
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Due to changes in the link to DAVID, will need to specify the correct url:
Found this to be true even with the current release of the DAVID Web Service tool (RDAVIDWebService_1.22.0)