UniProt database provides a list of controlled vocabulary represented as keywords for genes or proteins (https://www.uniprot.org/keywords/). This is useful for summarizing gene functions in a compact way. This package provides data of keywords hierarchy and gene-keywords relations.
If you want the latest version, install it directly from GitHub:
if (!requireNamespace("devtools", quietly = TRUE))
install.packages("devtools")
devtools::install_github("jokergoo/UniProtKeywords")First load the package:
library(UniProtKeywords)The package has five data objects. The first contains basic information of every keyword term:
data(kw_terms)
kw_terms[["Cell cycle"]]The other four contain hierarchical structures of the keyword terms:
data(kw_parents)
kw_parents[1:2]
data(kw_children)
kw_children[1:2]
data(kw_ancestors)
kw_ancestors[1:2]
data(kw_offspring)
kw_offspring[1:2]The UniProtKeywords package has also compiled genesets of keywords for some species, which can get by the function load_keyword_genesets().
The argument is the taxon ID of a species:
gl = load_keyword_genesets(9606)
gl[1:2]MIT @ Zuguang Gu