Use topGOdata in devtools package
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Entering edit mode
@emisecherre-23089
Last seen 9 months ago

Hello ! I'm trying to build a R devtools package, with this code :

ensembl = biomaRt::useMart("ensembl",dataset="hsapiens_gene_ensembl")
  goterm=biomaRt::getBM(attributes=c("hgnc_symbol",'go_id'), mart = ensembl) #mapping genes-go termes
  goterm=subset(goterm, !(goterm$go_id==""))
  goterm=subset(goterm, !(goterm$hgnc_symbol==""))

  gc=biomaRt::getBM(attributes=c("hgnc_symbol","entrezgene_id"),mart=ensembl) #mapping genes symbol - entrez genes id
  ensfull=gc$entrezgene_id[!is.na(gc$entrezgene_id))] #entrez genes existant pour l'humain
  ens=gprofiler2::gconvert(genes, organism="hsapiens", target='ENTREZGENE_ACC')$target #entrez gene de nos genes

  ensint=factor(as.integer(ensfull %in% ens))#preparation des donnees pour l'analyse GO
  names(ensint)=ensfull
  ensint
  #go termes enrichis BP
  GOdataBP <- methods::new("topGOdata", ontology = "BP", allGenes = ensint, annot = topGO::annFUN.org, mapping="org.Hs.eg.db", ID="entrez")
  resultFisBP <- topGO::runTest(GOdataBP, algorithm = "classic", statistic = "fisher")
  allResBP <- topGO::GenTable(GOdataBP, classic = resultFisBP, orderBy = "classic", ranksOf = "classic",topNodes=20)

The thing is, methods::new doesn't recognize the topGOdata Class, and add topGO::topGOdata doesn't fix the issue. Anyone know how to fix it ?

topGO devtools R • 144 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 1 hour ago
United States

You need to show the error you get. If it's something like this:

>  GOdata <- new("topGOdata",
                   ontology = "BP",
                   allGenes = geneList,
                   geneSel = topDiffGenes,
                   description = "GO analysis of ALL data: Differential Expression between B-cell and T-cell",
                   annot = annFUN.db,
                   affyLib = affyLib)
Error in getClass(Class, where = topenv(parent.frame())) : 
  "topGOdata" is not a defined class

That indicates that you haven't loaded the topGO package yet.

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Entering edit mode

It's exactly this error, the thing is that i can't use "library" to load topGO and i don't know an other way which works with devtools...

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Entering edit mode

Are you using roxygen2 to describe the imports of your package? If so, add

#' import topGO

to one of your source files, and add

Imports: topGO

to your descriptino file. Be sure to run devtools::document() to update the NAMESPACE, which should automatically include a line import(topGO).

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