enrichGO() error: unable to find an inherited method for function ‘keytypes’ for signature ‘"GRanges"’

Question

[Trinh]

I want to get data from AnnotationHub and cluster it. However, I have a error in the enrichGO(): Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘keytypes’ for signature ‘"GRanges"’

Please help me, thank you very much!

library(clusterProfiler) library(AnnotationHub) hub <- AnnotationHub() query(hub, "Candida albicans") CalbicansEntrez <- hub[["AH74041"]] head(CalbicansEntrez)

demo <- c("3635832", "30515194", "3636627")

enrichGO( demo, OrgDb = CalbicansEntrez, keyType = "ENTREZID",
ont = "BP", pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, qvalueCutoff = 0.2, minGSSize = 10, maxGSSize = 500, readable = TRUE, pool = FALSE )

[gglim]

Hi Trinh,

I checked the AnnotationHub R documentation Here.

You can try CalbicansEntrez <- makeTxDbFromGRanges(CalbicansEntrez) before using enrichGO().

[Trinh]

Thank you so much, I have add your code. I think it worked. However, another error appear: When I run the code, it cannot match with keytype. I check the keytype and change to Genename, GeneID... however, it's not work.

If you know how to get the right keyType from ENTREZID or Genenames (B9J08_001380, B9J08_004112, B9J08_002819, B9J08_003276) for it, please help me.

library(rtracklayer) library(GenomicRanges) library(GenomicFeatures) library(clusterProfiler) library(AnnotationHub) hub <- AnnotationHub() query(hub, "Candida albicans") CalbicansEntrez <- hub[["AH74123"]] head(CalbicansEntrez) CalbicansEntrez <- makeTxDbFromGRanges(CalbicansEntrez)

demo <- c("3636627", "3643917", "3646558")

keytypes(CalbicansEntrez)

enrichGO( demo, OrgDb = CalbicansEntrez, keyType = "GENEID",
ont = "BP", pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, qvalueCutoff = 0.2, minGSSize = 10, maxGSSize = 500, readable = TRUE, pool = FALSE )

Error in testForValidKeytype(x, keytype) : Invalid keytype: GOALL. Please use the keytypes method to see a listing of valid arguments.

[gglim]

I repeated your code and got the same error. I think it's because the CalbicansEntrez doesn't have enough annotation info.

As you might have noticed that the output of keytypes() shows only...

keytypes(CalbicansEntrez) 
[1] "CDSID"    "CDSNAME"  "EXONID"   "EXONNAME" "GENEID"   "TXID"     "TXNAME"

For details you can use functions like genes(), transcripts(), exons() to check

> genes(CalbicansEntrez) %>% head
GRanges object with 6 ranges and 1 metadata column:
                            seqnames      ranges strand |     gene_id
                               <Rle>   <IRanges>  <Rle> | <character>
  C1_00010W_B Ca22chr1B_C_albicans..   4059-4397      + | C1_00010W_B
  C1_00020C_B Ca22chr1B_C_albicans..   4409-4720      - | C1_00020C_B
  C1_00030C_B Ca22chr1B_C_albicans..   8597-8908      - | C1_00030C_B
  C1_00040W_B Ca22chr1B_C_albicans.. 10718-11485      + | C1_00040W_B
  C1_00050C_B Ca22chr1B_C_albicans.. 11648-11995      - | C1_00050C_B
  C1_00060W_B Ca22chr1B_C_albicans.. 12163-13701      + | C1_00060W_B
  -------
  seqinfo: 8 sequences from FungiDB-45_CalbicansSC5314_B genome; no seqlengths

...and you will find there's no enough annotation for your demo.

FYI there's a similar question answered by GC.Yu (developer of clusterProfiler) here you can take a look.

BTW you can use query(hub, "Candida albicans") %>% display to choose your database, for instance "AH74762" is in TxDb format so the makeTxDbFromGRanges part can be ommited.

[Trinh]

I also repeat my code with demo 3 genes having in the database. It continue to have the same error. :(

C1_00010W_B Ca22chr1B_C_albicans.. 4059-4397 + | C1_00010W_B
C1_00020C_B Ca22chr1B_C_albicans.. 4409-4720 - | C1_00020C_B
C1_00030C_B Ca22chr1B_C_albicans.. 8597-8908 - | C1_00030C_B