Im trying to develop a shiny app to run an Gene Ontology analysis with the topGO package (https://bioconductor.org/packages/release/bioc/html/topGO.htm)
If i run the script to do the analysis in local machine out of shiny , the gene analysis runs fine, problem is when I implemented the analysis in a shiny app and got a "topGodata class is not defined" error.
Here are my code:
#server
#geneID function
geneID <- reactive ({
geneid <- rownames(results())
return(geneid)
})
#interesting genes list
myInterestingGenes <- reactive({
myInterestingGenes <- rownames(selected())
return(myInterestingGenes)
})
#genelist for go function
geneList <- reactive({
geneList <- factor(as.integer(geneID() %in% myInterestingGenes()))
names(geneList) <- geneID()
return(geneList)
})
#create topGodata objetc
godata <- reactive({
topgo<- new(Class = "topGodata", ontology ="BP", allGenes = geneList(),
nodeSize =10, annot = annFUN.db, affyLib = "clariomshumantranscriptcluster.db")
})
#print topGO object
output$topgo <- renderText({
godata()
})
I am able to print the list of genes from geneList() function, but when I try to define the topGodata object I get the not define class error