Issue with ORA and importCP

[zganjarmia]

Hi, Firstly, kudos for the development of genekitr. It's a great tool and your reasons for its creation resonate so much with my experiences so far.

I'm currently working with the organism Yarrowia lipolytica and have noted some challenges:

1. The geneset for Yarrowia lipolytica is available in the geneset package (GO and KEGG), but there is no organism value attached to it when running getGO:

   > mf <- getGO(org = "Yarrowia lipolytica", ont = "mf")
   > head(mf$geneset)
         mf          gene
   1 GO:0000030 YALI0_C04004g
   2 GO:0000030 YALI0_D10549g
   3 GO:0000030 YALI0_B01672g
   4 GO:0000030 YALI0_E02222g
   5 GO:0000030 YALI0_A20922g
   6 GO:0000030 YALI0_A13585g
   > head(mf$geneset_name)
         id                           name
   1 GO:0000030   mannosyltransferase activity
   2 GO:0000049                   tRNA binding
   3 GO:0000149                  SNARE binding
   4 GO:0000166             nucleotide binding
   5 GO:0000175 3'-5'-RNA exonuclease activity
   6 GO:0000287          magnesium ion binding
   > mf$organism
   [1] NA

2. However, I ran into issues with follow-up functions, specifically the genORA function. It suggests there's no short name for the organism. This is perplexing given the initial inclusion of Yarrowia lipolytica in the geneset. I also tried to add the organism value, but the function still does not work.

   >   gs <- genORA(de.genes$ensembl_gene_id, mf$geneset,padj_method = "BH",
   +                p_cutoff = 0.05,)
   Error in if (organism == "hg" | organism == "human" | organism == "hsa" |  : 
   argument is of length zero

3. I also tried a different route, performing the ORA with ClusterProfiler and then importing the results to genekitr. But this too resulted in an error.

   >   ora_go <- clusterProfiler::enrichGO(gene = de.genes,
   +                         OrgDb = org.Ylipolytica.eg.db,
   +                         universe = filtered_data$entrez,
   +                         keyType = "ENTREZID",  
   +                         ont = "ALL",  # Biological Process
   +                         pAdjustMethod = "BH",  # adjust method
   +                         pvalueCutoff = 0.05,
   +                         minGSSize = 5,
   +                         maxGSSize = 500,
   +                         readable = FALSE)
   >   go_easy <- importCP(ora_go, type = "go")
   Error in mapEnsOrg(object@organism) : 
   Check the latin_short_name in `genekitr::ensOrg_name`

   I'd appreciate any insights or suggestions you might have regarding these issues. Is there a workaround or am I possibly missing a step? Thanks!

[reedliu]

Hi, I have fixed the ORA issue and please update packages (geneset >= 0.2.8 and genekitr >= 1.2.5 ).

# test code
library(geneset)
mf <- getGO(org = "Yarrowia lipolytica", ont = "mf")
mf$organism
# "yarrowia"

library(genekitr)
id <- mf$geneset$gene[1:50]
ora <- genORA(id, mf,padj_method = "BH",p_cutoff = 0.05)

Then, you could pass the ora result to plot function:

# example
plotEnrich(ora, plot_type = "dot")

For the third question, could you send me the org.Ylipolytica.eg.db so I can reproduce and test?

[reedliu]

I will close the issue now. If you have any further feedback, please open this issue again.