Cannabis OrgDb
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Entering edit mode
@68c324c6
Last seen 21 days ago
Brazil

Hello guys.

I want to download cannabis orgdb using AnnotationHub, but when I try to use at enrichGO and others packages it doesn't work. What I can do?

> library(AnnotationHub)

> hub <- AnnotationHub()

snapshotDate(): 2023-10-23

> query(hub, c("cannabis","orgdb"))

AnnotationHub with 1 record
# snapshotDate(): 2023-10-23
# names(): AH114845
# $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Cannabis sativa
# $rdataclass: OrgDb
# $rdatadateadded: 2023-10-20
# $title: org.Cannabis_sativa.eg.sqlite
# $description: NCBI gene ID based annotations about Cannabis sativa
# $taxonomyid: 3483
# $genome: NCBI genomes
# $sourcetype: NCBI/UniProt
# $sourceurl: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/, ftp://ftp.uniprot.org/pub/databases/uniprot/current_rele...
# $sourcesize: NA
# $tags: c("NCBI", "Gene", "Annotation") 
# retrieve record with 'object[["AH114845"]]' 

> org.Cs.eg.db <- hub[["AH114845"]]

> org.Cs.eg.db

> columns(org.Cs.eg.db)

OrgDb object:
| DBSCHEMAVERSION: 2.1
| DBSCHEMA: NOSCHEMA_DB
| ORGANISM: Cannabis sativa
| SPECIES: Cannabis sativa
| CENTRALID: GID
| Taxonomy ID: 3483
| Db type: OrgDb
| Supporting package: AnnotationDbi

Here my script for comparecluster:

> compareCluster(
  geneClusters = ortologos_filtrados,
  fun = "enrichGO",
  data = "hub",
  source_from = NULL,
)
Error in fun(i, ...) : argument "OrgDb" is missing, with no default
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware • 136 views
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1
Entering edit mode
Guido Hooiveld ★ 4.0k
@guido-hooiveld-2020
Last seen 15 hours ago
Wageningen University, Wageningen, the …
> library(AnnotationHub)
> hub <- AnnotationHub()
snapshotDate(): 2023-10-23
> query(hub,  c("cannabis","orgdb") )
AnnotationHub with 1 record
# snapshotDate(): 2023-10-23
# names(): AH114845
# $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Cannabis sativa
# $rdataclass: OrgDb
# $rdatadateadded: 2023-10-20
# $title: org.Cannabis_sativa.eg.sqlite
# $description: NCBI gene ID based annotations about Cannabis sativa
# $taxonomyid: 3483
# $genome: NCBI genomes
# $sourcetype: NCBI/UniProt
# $sourceurl: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/, ftp://ftp.uniprot.org/p...
# $sourcesize: NA
# $tags: c("NCBI", "Gene", "Annotation") 
# retrieve record with 'object[["AH114845"]]' 
> 
> 
> org.Cs.eg.db <- hub[["AH114845"]]
loading from cache
> 
> columns(org.Cs.eg.db)
 [1] "ACCNUM"      "ALIAS"       "CHR"         "ENTREZID"    "EVIDENCE"   
 [6] "EVIDENCEALL" "GENENAME"    "GID"         "GO"          "GOALL"      
[11] "ONTOLOGY"    "ONTOLOGYALL" "PMID"        "REFSEQ"      "SYMBOL"     
> 
> k <- keys(org.Cs.eg.db)
> length(k)
[1] 31441
> 
> 
> ## run enrichGO with the 1st 500 keys/genes (out of 31441)
> library(clusterProfiler)
> 
> ego <- enrichGO(gene          = k[1:500],
+                 OrgDb         = org.Cs.eg.db,
+                 ont           = "ALL",
+                 pAdjustMethod = "BH",
+                 pvalueCutoff  = 0.01,
+                 qvalueCutoff  = 0.05,
+                 readable      = TRUE)
> 
> ego
#
# over-representation test
#
#...@organism    Cannabis sativa 
#...@ontology    GOALL 
#...@keytype     ENTREZID 
#...@gene        chr [1:500] "23630667" "23630669" "23630670" "23630672" "23630673" ...
#...pvalues adjusted by 'BH' with cutoff <0.01 
#...9 enriched terms found
'data.frame':   9 obs. of  10 variables:
 $ ONTOLOGY   : chr  "BP" "CC" "CC" "CC" ...
 $ ID         : chr  "GO:0015979" "GO:0009507" "GO:0009536" "GO:0009579" ...
 $ Description: chr  "photosynthesis" "chloroplast" "plastid" "thylakoid" ...
 $ GeneRatio  : chr  "58/147" "172/172" "172/172" "71/172" ...
 $ BgRatio    : chr  "58/173" "173/207" "177/207" "72/207" ...
 $ pvalue     : num  8.29e-06 3.29e-38 2.60e-31 1.38e-06 6.89e-06 ...
 $ p.adjust   : num  4.23e-04 1.71e-36 6.77e-30 2.39e-05 7.16e-05 ...
 $ qvalue     : num  4.23e-04 1.35e-36 5.34e-30 1.89e-05 5.66e-05 ...
 $ geneID     : chr  "psbA/psbK/psbI/petN/psbM/psbD/psbC/lhbA/psaB/psaA/ycf3/rbcL/psaI/ycf4/petA/psbJ/psbL/psbF/psbE/petL/petG/psaJ/p"| __truncated__ "psbA/matK/rps16/psbK/psbI/atpA/atpF/atpH/atpI/rps2/rpoC2/rpoC1/rpoB/petN/psbM/psbD/psbC/lhbA/rps14/psaB/psaA/yc"| __truncated__ "psbA/matK/rps16/psbK/psbI/atpA/atpF/atpH/atpI/rps2/rpoC2/rpoC1/rpoB/petN/psbM/psbD/psbC/lhbA/rps14/psaB/psaA/yc"| __truncated__ "psbA/psbK/psbI/atpF/petN/psbM/psbD/psbC/lhbA/psaB/psaA/ycf3/ndhK/atpE/psaI/ycf4/petA/psbJ/psbL/psbF/psbE/petL/p"| __truncated__ ...
 $ Count      : int  58 172 172 71 65 65 123 123 40
#...Citation
 T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu.
 clusterProfiler 4.0: A universal enrichment tool for interpreting omics data.
 The Innovation. 2021, 2(3):100141 

> 
> as.data.frame(ego)[1:5,]
           ONTOLOGY         ID             Description GeneRatio BgRatio
GO:0015979       BP GO:0015979          photosynthesis    58/147  58/173
GO:0009507       CC GO:0009507             chloroplast   172/172 173/207
GO:0009536       CC GO:0009536                 plastid   172/172 177/207
GO:0009579       CC GO:0009579               thylakoid    71/172  72/207
GO:0034357       CC GO:0034357 photosynthetic membrane    65/172  66/207
                 pvalue     p.adjust       qvalue
GO:0015979 8.287967e-06 4.226863e-04 4.226863e-04
GO:0009507 3.291786e-38 1.711729e-36 1.351365e-36
GO:0009536 2.602098e-31 6.765454e-30 5.341148e-30
GO:0009579 1.377601e-06 2.387842e-05 1.885138e-05
GO:0034357 6.887853e-06 7.163368e-05 5.655290e-05
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        geneID
GO:0015979                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   psbA/psbK/psbI/petN/psbM/psbD/psbC/lhbA/psaB/psaA/ycf3/rbcL/psaI/ycf4/petA/psbJ/psbL/psbF/psbE/petL/petG/psaJ/psbT/psbN/psbH/petB/petD/psaC/ycf3/psaA/psbB/psbT/psaC/rbcL/psaI/petD/psbC/psbJ/petA/psaB/petL/petB/psbI/psbH/psbL/psbE/psbF/ycf4/psbN/petG/psbM/psbZ/petN/psbA/psaJ/psbK/psbD/psbB
GO:0009507 psbA/matK/rps16/psbK/psbI/atpA/atpF/atpH/atpI/rps2/rpoC2/rpoC1/rpoB/petN/psbM/psbD/psbC/lhbA/rps14/psaB/psaA/ycf3/rps4/ndhJ/ndhK/ndhC/atpE/atpB/rbcL/accD/psaI/ycf4/cemA/petA/psbJ/psbL/psbF/psbE/petL/petG/psaJ/rpl33/rps18/rpl20/rps12/psbT/psbN/psbH/petB/petD/rpoA/rps11/rpl36/rps8/rpl14/rpl16/rps3/rpl22/rps19/rpl2/rpl23/ycf2/ndhB/rps7/ycf1/ndhF/rpl32/ccsA/ndhD/psaC/ndhE/ndhG/ndhI/ndhA/ndhH/rps15/rps7/ndhB/ycf2/rpl23/rpl2/rps19/clpP/rps12/rps12/clpP/rpoC1/rpoB/ndhH/rpl32/ycf3/rps7/psaA/psbB/psbT/rps16/atpF/rpl23/rps19/psaC/rbcL/psaI/accD/petD/rps3/atpH/rpoA/rps15/ndhF/psbC/rps11/psbJ/ndhD/rps2/rpoC2/petA/ndhC/rpl22/cemA/ndhI/ndhA/ndhK/ndhB/rpl36/rpl14/atpB/rps19/rpl16/rps12/rpl20/ndhG/psaB/rpl2/rpl2/ycf1/petL/atpI/ndhE/petB/rps18/psbI/psbH/rpl33/psbL/psbE/psbF/ycf4/rps8/psbN/petG/psbM/atpA/matK/psbZ/rps4/petN/ndhB/ycf2/ccsA/psbA/rps14/psaJ/ycf2/rpl23/ndhJ/atpE/psbK/psbD/ycf1/rps7/psbB/ycf1
GO:0009536 psbA/matK/rps16/psbK/psbI/atpA/atpF/atpH/atpI/rps2/rpoC2/rpoC1/rpoB/petN/psbM/psbD/psbC/lhbA/rps14/psaB/psaA/ycf3/rps4/ndhJ/ndhK/ndhC/atpE/atpB/rbcL/accD/psaI/ycf4/cemA/petA/psbJ/psbL/psbF/psbE/petL/petG/psaJ/rpl33/rps18/rpl20/rps12/psbT/psbN/psbH/petB/petD/rpoA/rps11/rpl36/rps8/rpl14/rpl16/rps3/rpl22/rps19/rpl2/rpl23/ycf2/ndhB/rps7/ycf1/ndhF/rpl32/ccsA/ndhD/psaC/ndhE/ndhG/ndhI/ndhA/ndhH/rps15/rps7/ndhB/ycf2/rpl23/rpl2/rps19/clpP/rps12/rps12/clpP/rpoC1/rpoB/ndhH/rpl32/ycf3/rps7/psaA/psbB/psbT/rps16/atpF/rpl23/rps19/psaC/rbcL/psaI/accD/petD/rps3/atpH/rpoA/rps15/ndhF/psbC/rps11/psbJ/ndhD/rps2/rpoC2/petA/ndhC/rpl22/cemA/ndhI/ndhA/ndhK/ndhB/rpl36/rpl14/atpB/rps19/rpl16/rps12/rpl20/ndhG/psaB/rpl2/rpl2/ycf1/petL/atpI/ndhE/petB/rps18/psbI/psbH/rpl33/psbL/psbE/psbF/ycf4/rps8/psbN/petG/psbM/atpA/matK/psbZ/rps4/petN/ndhB/ycf2/ccsA/psbA/rps14/psaJ/ycf2/rpl23/ndhJ/atpE/psbK/psbD/ycf1/rps7/psbB/ycf1
GO:0009579                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  psbA/psbK/psbI/atpF/petN/psbM/psbD/psbC/lhbA/psaB/psaA/ycf3/ndhK/atpE/psaI/ycf4/petA/psbJ/psbL/psbF/psbE/petL/petG/psaJ/psbT/psbN/psbH/petB/petD/ndhF/ccsA/ndhD/psaC/ndhG/ndhI/ycf3/psaA/psbB/psbT/psaC/psaI/petD/ndhF/psbC/psbJ/ndhD/petA/ndhI/ndhK/ndhG/psaB/petL/petB/psbI/psbH/psbL/psbE/psbF/ycf4/psbN/petG/psbM/psbZ/petN/ccsA/psbA/psaJ/atpE/psbK/psbD/psbB
GO:0034357                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                psbA/psbK/psbI/atpF/petN/psbM/psbD/psbC/lhbA/psaB/psaA/ycf3/psaI/ycf4/petA/psbJ/psbL/psbF/psbE/petL/petG/psaJ/psbT/psbN/psbH/petB/petD/ndhF/ccsA/ndhD/psaC/ndhG/ycf3/psaA/psbB/psbT/psaC/psaI/petD/ndhF/psbC/psbJ/ndhD/petA/ndhG/psaB/petL/petB/psbI/psbH/psbL/psbE/psbF/ycf4/psbN/petG/psbM/psbZ/petN/ccsA/psbA/psaJ/psbK/psbD/psbB
           Count
GO:0015979    58
GO:0009507   172
GO:0009536   172
GO:0009579    71
GO:0034357    65
> 
> 
> 
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