OrgDb for maize
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sansan • 0
@d5e5b958
Last seen 5 weeks ago
Mexico

Hello,

I am trying to perform a GO analysis with clusterProfiler, however I am having problems with OrgDb because it is not supported, could anyone suggest something to resolve this?

ora_analysis_BP <- enrichGO(
  gene = annot_diff$entrezgene_id,
  universe = annot_universe$entrezgene_id,
  OrgDb=maize ,
  keyType = "ENTREZID",
  ont = "CC",
  pAdjustMethod = "BH",
  qvalueCutoff = 0.05,
  readable = TRUE,
  pool = FALSE
)

Update:

I solved my problem with AnnotationHub:

https://guangchuangyu.github.io/cn/2017/07/clusterprofiler-maize/#disqus_thread

Thanks.

clusterProfiler OrgDb biomaRt Zea_mays • 240 views
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Guido Hooiveld ★ 4.0k
@guido-hooiveld-2020
Last seen 1 hour ago
Wageningen University, Wageningen, the …

I notice the data you are working with is based on ensembl ids. This is important, because the OrgDb are annotation databases that are NCBI entrez centered. In those cases it would be best to stay in the 'ensembl world'.

Please check my post at the clusterProfiler GitHub for some code to do this: https://github.com/YuLab-SMU/clusterProfiler/issues/588#issuecomment-1600652905

Note that you will have to modify it slightly because I used it to analyze an ensembl-based tomato dataset.

<<added>>: the original post is now edited, so it is not clear anymore that the dataset was ensembl-based.

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@james-w-macdonald-5106
Last seen 1 hour ago
United States
> library(AnnotationHub)

> hub <- AnnotationHub()
  |===========================| 100%

snapshotDate(): 2023-10-23

> query(hub, c("zea","orgdb"))
AnnotationHub with 5 records
# snapshotDate(): 2023-10-23
# $dataprovider: ftp://ftp.ncbi.n...
# $species: Zea mays_var._japonic...
# $rdataclass: OrgDb
# additional mcols():
#   taxonomyid, genome,
#   description,
#   coordinate_1_based,
#   maintainer, rdatadateadded,
#   preparerclass, tags,
#   rdatapath, sourceurl,
#   sourcetype 
# retrieve records with, e.g.,
#   'object[["AH114308"]]' 


  AH114308 |
  AH114309 |
  AH115861 |
  AH115862 |
  AH115863 |
           title                   
  AH114308 org.Zea_mays.eg.sqlite  
  AH114309 org.Zea_mays_var._jap...
  AH115861 org.Helicoverpa_zea.e...
  AH115862 org.Heliothis_zea.eg....
  AH115863 org.Phalaena_zea.eg.s...
> org.Zm.eg.db <- hub[["AH114308"]]
downloading 1 resources
retrieving 1 resource
  |===========================| 100%

loading from cache

> org.Zm.eg.db
OrgDb object:
| DBSCHEMAVERSION: 2.1
| DBSCHEMA: NOSCHEMA_DB
| ORGANISM: Zea mays
| SPECIES: Zea mays
| CENTRALID: GID
| Taxonomy ID: 4577
| Db type: OrgDb
| Supporting package: AnnotationDbi

Please see: help('select') for usage information
> columns(org.Zm.eg.db)
 [1] "ACCNUM"      "ALIAS"      
 [3] "CHR"         "ENTREZID"   
 [5] "EVIDENCE"    "EVIDENCEALL"
 [7] "GENENAME"    "GID"        
 [9] "GO"          "GOALL"      
[11] "ONTOLOGY"    "ONTOLOGYALL"
[13] "PMID"        "REFSEQ"     
[15] "SYMBOL"      "UNIGENE"

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