I was trying to use OrganismDbi package to build an annotation package for osativa indica.
I used the following code chunk but it throws an error at the end
library(OrganismDbi) oindica <- makeOrganismDbFromBiomart(biomart="plants_mart", dataset="oindica_eg_gene", transcript_ids=NULL, circ_seqs=NULL, filter="", id_prefix="ensembl_", host="plants.ensembl.org", port=80, miRBaseBuild=NA, keytype = "ENSEMBL", orgdb = NA)
Download and preprocess the 'transcripts' data frame ... OK Download and preprocess the 'chrominfo' data frame ... OK Download and preprocess the 'splicings' data frame ... OK Download and preprocess the 'genes' data frame ... OK Prepare the 'metadata' data frame ... Error in GenomeInfoDb:::lookup_tax_id_by_organism(organism) : Oryza indica: unknown organism. Please use 'loadTaxonomyDb()' to see viable genus/species and taxonomy IDs.
How can I inform GenomeInfoDb about the correct Taxon-ID of oryza? I need this package to run clusterprofiler package for GO term analysis.
GenomeInfoDb:::lookup_tax_id_by_organism(organism) does not work and lacks manual for reference.