Convert gene identifiers with AnnotationHub

map_gene_annot() Maps gene annotations using OrgDb databases from AnnotationHub. Most useful for mapping gene identifiers. This function can pick one mapped annotation for each key.

map_gene_annot(taxonomy_id = 9606, keys = "TP53",
  columns = c("ENSEMBL"), keytype = "SYMBOL", pick_one = TRUE,
  localHub = FALSE, return_org_db = FALSE,
  ann_hub_cache = AnnotationHub::getAnnotationHubOption("CACHE"))

Arguments

taxonomy_id

Taxonomy id of your species. 9606 is human, 10090 is mouse. Find your species id using taxonomy search by UniProt: https://www.uniprot.org/taxonomy/.
keys

gene or protein identifiers of keytype
columns

columns to retrieve. Details: colsAndKeytypes.
keytype

type of keys identifiers. Use keytypes(map_gene_annot(taxonomy_id = 9606, return_org_db = T)) to find which keytypes are available. Most frequent options: "ENSEMBL", "SYMBOL", "ALIAS".
pick_one

pick one mapped annotation (from columns) for each key. Works only with one column.
localHub

set localHub = FALSE for working offline. Details AnnotationHub.
return_org_db

return OrgDb database link instead of gene annotations.
ann_hub_cache

If needed, set location of local AnnotationHub cache to specific directory by providing it here. To view where cache is currently located use getAnnotationHubOption("CACHE")

Value

data.frame containing mapped identifiers