R/data.R

In ontologySimilarity: Calculating Ontological Similarities

#' @name gene_GO_terms 
#' @title Gene Ontology annotation of genes
#' @description \code{list} object containing character vectors of term IDs of GO terms annotating each gene, named by gene. Users can select a list of annotations for a subset of the annotated genes using a character vector of gene symbols, e.g. \code{gene_GO_terms[c("ACTN1", "TUBB1")]}, which can then be used in functions for calculating similarities, e.g. \code{\link{get_sim_grid}}. Note that these annotation vectors contain annotation from all major branches of the Gene Ontology, however one can simply extract the terms only relevant to one by calling the function in the \code{ontologyIndex} package: \code{intersection_with_descendants}. 
#' @docType data
#' @format List of character vectors.
#' @references Annotation downloaded from Gene Ontology consortium website, http://geneontology.org/, dated 20/02/2024.
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#' @name GO_IC 
#' @title Gene Ontology terms information content.
#' @description Numeric vector containing the information content of Gene Ontology terms based on frequencies of annotation data object \code{gene_GO_terms}. The object can be derived using the function \code{get_term_info_content} and data object \code{go} from the \code{ontologyIndex} package.
#' @docType data
#' @format List of character vectors.
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