Obtain GO term annotations for proteins — get_go

Given a set of UniProt IDs, this function queries UniProt to obtain the annotated GO terms. Optionally, these GO terms can be expanded to include all ancestors too, which can be helpful when using GO over-representation/enrichment tools that do not consider the GO term heirarchy. Note that expansion will significantly increase the run-time

Usage

get_go_terms(UniprotID, expand_terms = FALSE, verbosity = 0)

Arguments

expand_terms: logical Should GO terms be expanded to include all ancestors
verbosity: integer Verbosity level for uniprotREST::uniprot_map
uniprotIDs: character vector Uniprot IDs

Value

data.frame object.

Examples

uniprotIDs <- c('O76024', 'Q03135', 'Q96T23')
get_go_terms(uniprotIDs, expand_terms=TRUE)
#> Error in (function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called ‘GO.db’",     call = loadNamespace(x), package = "GO.db", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition"))): error in evaluating the argument 'x' in selecting a method for function 'select': there is no package called ‘GO.db’