clusterProfiler: Which GO version is used behind ?
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ZheFrench ▴ 20
@zhefrench-11689
Last seen 13 hours ago
France

I'm using clusterProfiler v3.2.14 for GO molecular function in human. 

The background size is 16309.

Panther webtool give a size of 21002. Annotation Version and Release Date: GO Ontology database Released 2017-08-14

I was wondering which version of the GO database is use in ClusterProfiler. Why these numbers are differents ?

I'm using something like.

edb = useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",host="jul2016.archive.ensembl.org")

gene_infos = getBM(attributes=c('ensembl_gene_id','hgnc_symbol','gene_biotype','chromosome_name','start_position','end_position','strand','entrezgene'),values=data[,opt$column],filters='ensembl_gene_id',mart=edb)

# SET INPUT LIST
entrez_id  <- gene_infos$entrezgene
ensembl_id <- gene_infos$ensembl_gene_id

go_mf <- enrichGO(gene=entrez_id,OrgDb = org.Hs.eg.db,ont = "MF",pvalueCutoff = 0.01, pAdjustMethod = "BH", qvalueCutoff = 0.05, readable = TRUE)

 

 


 

 
clusterProfiler • 2.3k views
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Guido Hooiveld ★ 3.0k
@guido-hooiveld-2020
Last seen 1 day ago
Wageningen University, Wageningen, the …

AFAIK clusterProfiler uses under the hood the GO information available in the library GO.db. This GO annotation database is updated twice a year before each new Bioconductor release. Assuming you are using the latest Bioconductor release (i.e. 3.5), then the GO data was collected on 29 March 2017 (GO.db version 3.4.1).

> library(clusterProfiler)
> library(GO.db)

> GO.db
GODb object:
| GOSOURCENAME: Gene Ontology
| GOSOURCEURL: ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
| GOSOURCEDATE: 2017-Mar29
| Db type: GODb
| package: AnnotationDbi
| DBSCHEMA: GO_DB
| GOEGSOURCEDATE: 2017-Mar29
| GOEGSOURCENAME: Entrez Gene
| GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
| DBSCHEMAVERSION: 2.1

Please see: help('select') for usage information
>

 

> sessionInfo()
R version 3.4.1 Patched (2017-08-27 r73149)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
[1] GO.db_3.4.1           AnnotationDbi_1.38.2  IRanges_2.10.3       
[4] S4Vectors_0.14.3      Biobase_2.36.2        BiocGenerics_0.22.0  
[7] clusterProfiler_3.4.4 DOSE_3.2.0           

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12        compiler_3.4.1      plyr_1.8.4         
 [4] tools_3.4.1         digest_0.6.12       bit_1.1-12         
 [7] RSQLite_2.0         memoise_1.1.0       tibble_1.3.4       
[10] gtable_0.2.0        pkgconfig_2.0.1     rlang_0.1.2        
[13] fastmatch_1.1-0     igraph_1.1.2        DBI_0.7            
[16] rvcheck_0.0.9       fgsea_1.2.1         gridExtra_2.2.1    
[19] stringr_1.2.0       bit64_0.9-7         grid_3.4.1         
[22] glue_1.1.1          qvalue_2.8.0        data.table_1.10.4  
[25] BiocParallel_1.10.1 GOSemSim_2.2.0      purrr_0.2.3        
[28] tidyr_0.7.1         ggplot2_2.2.1       DO.db_2.9          
[31] reshape2_1.4.2      blob_1.1.0          magrittr_1.5       
[34] splines_3.4.1       scales_0.5.0        colorspace_1.3-2   
[37] stringi_1.1.5       lazyeval_0.2.0      munsell_0.4.3      
>

 

 

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By the way ,same question for Reactome ? and Kegg ? I think enrichKEGG use lastest remote version using use_internal_data=FALSE.

Is there a way to upgrade these anotations  without upgrading R bioconductor. I'm stuck to R 3.3.1 and can't upgrage bioconductor withtout reinstalling a more recent version of R.

 

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You can always install whatever version of package you want - that's the beauty of R and Open Source software in general.

However, do note that we don't support anything but the release version of R/BioC, which means if you are running some non-standard configuration and you have problems, it's on you to fix. If you post a question here with a sessionInfo output that indicates you are mixing and matching, the first response will be to tell you to install the latest version of R/BioC.

 

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