OrgDb for maize
2
@d5e5b958
Last seen 6 months 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
• 713 views
@guido-hooiveld-2020
Last seen 4 hours 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.
@james-w-macdonald-5106
Last seen 26 minutes 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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