##'termSim
##'
##'measuring similarities between two term vectors.
##'
##'provide two term vectors, this function will calculate their similarities.
##'
##'@param t1 term vector
##'@param t2 term vector
##'@param method one of "Wang", "Resnik", "Rel", "Jiang", and "Lin", "TCSS".
##'@param semData GOSemSimDATA object
##'@return score matrix
##'@export
##'@author Guangchuang Yu \url{http://guangchuangyu.github.io}
termSim <- function(t1,
t2,
semData,
method=c("Wang","Resnik","Rel","Jiang","Lin", "TCSS")
) {
method <- match.arg(method)
if (all(is.na(t1)) || all(is.na(t2)))
return(NA)
t1 <- t1[!is.na(t1)]
t2 <- t2[!is.na(t2)]
## genes in cluster may share go terms,
## and should affect similarity of clusters in clusterSim and mclusterSim.
##
## t1 <- unique(t1)
## t2 <- unique(t2)
if ( method %in% c("Resnik", "Jiang", "Lin", "Rel") ) {
return(infoContentMethod(t1, t2, method = method, semData))
} else if (method == "Wang") {
return(wangMethod(t1, t2, semData@ont))
} else if ( method == "TCSS" ) {
return(tcssMethod(t1, t2, semData))
}
}
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