R/meshSim.R

In GuangchuangYu/meshes: MeSH Enrichment and Semantic analyses

##' semantic similarity between two MeSH term vectors
##'
##' 
##' @title meshSim
##' @param meshID1 MeSH term vector 
##' @param meshID2 MeSH term vector 
##' @param measure one of "Wang", "Resnik", "Rel", "Jiang" and "Lin"
##' @param semData annotation data for semantic measurement, output by meshdata function 
##' @return score matrix
##' @importFrom GOSemSim termSim
##' @export
##' @examples
##' ## library(meshes)
##' ## library(AnnotationHub)
##' ## ah <- AnnotationHub()
##' ## qr_hsa <- query(ah, c("MeSHDb", "Homo sapiens"))
##' ## filepath_hsa <- qr_hsa[[1]]
##' ## db <- MeSHDbi::MeSHDb(filepath_hsa)
##' ## hsamd <- meshdata(db, category='A', computeIC=T, database="gendoo")
##' data(hsamd)
##' meshSim("D000009", "D009130", semData=hsamd, measure="Resnik")
##' @author Guangchuang Yu \url{https://guangchuangyu.github.io}
meshSim <- function(meshID1,
                    meshID2,
                    measure = "Wang",
                    semData) {
    if (!exists(".meshesEnv")) .initial()
    
    scores <- termSim(meshID1, meshID2, semData, measure)
    if(nrow(scores) == 1 & ncol(scores) == 1)
        scores <- as.numeric(scores)
    return(scores)
}