Cannabis OrgDb
1
@68c324c6
Last seen 7 months 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
• 377 views
@guido-hooiveld-2020
Last seen 6 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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