ViSEAGO tutorial: visualising topGO object

问题

Earlier, I had posted a question and was able to load in my data successfully and create a topGO object after some help. I'm trying to visualise GO terms that are significantly associated with the list of differentially expressed genes that I have from mouse RNA-seq data.

Now, I'd want to raise a concern about ViSEAGO's tutorial. The tutorial initially specifies loading two files: 'selection.txt' and 'background.txt'. The origin of these files is not clearly stated. However, after a lot of digging into topGO's documentation, I was able to find the datatypes for each of the files. But, even after following these, I have a problem running the following code. Does anyone have any insights to share?

WORKING CODE:

mysampleGOdata <- new("topGOdata",
                      description = "my Simple session",
                      ontology = "BP",
                      allGenes = geneList_new,
                      nodeSize = 1,
                      annot = annFUN.org,
                      mapping="org.Mm.eg.db", 
                      ID = "SYMBOL")

resultFisher <- runTest(mysampleGOdata, algorithm = "classic", statistic = "fisher")

head(GenTable(mysampleGOdata,fisher=resultFisher),20)

myNewBP<-GenTable(mysampleGOdata,fisher=resultFisher)

PROBLEMS:

> head(myNewBP,2)
       GO.ID                      Term Annotated Significant Expected  fisher
1 GO:0006006 glucose metabolic process       194          12     0.19 1.0e-19
2 GO:0019318  hexose metabolic process       223          12     0.22 5.7e-19

> ###################
> # merge results
> myBP_sResults<-ViSEAGO::merge_enrich_terms(
+   Input=list(
+     condition=c("mysampleGOdata","resultFisher")
+   )
+ )
Error in setnames(x, value) : 
  Can't assign 3 names to a 2 column data.table
> myNewBP<-GenTable(mysampleGOdata,fisher=resultFisher)
> ###################
> # display the merged table
> ViSEAGO::show_table(myNewBP)
Error in ViSEAGO::show_table(myNewBP) : 
  object must be enrich_GO_terms, GO_SS, or GO_clusters class objects

According to the tutorial, the printed table contains for each enriched GO terms, additional columns including the list of significant genes and frequency (ratio of the number of significant genes to the number of background genes) evaluated by comparison. I think I have that, but it's definitely not working.

Can someone see why? I'm not very clear on this. Thanks!

来源：https://stackoverflow.com/questions/59653531/viseago-tutorial-visualising-topgo-object

标签

data-visualization

ontology

rna-seq