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#' Show the methods for calculating correlation or distance
#' @description This function outputs the methods available for the calculation of
#' the correlation or distance. The standard correlation methods use stats::cor and
#' a wide variety of distance methods are available using the philentropy package.
#' To be used as input in \code{\link{calculate_expression_similarity_counts}} or
#' \code{\link{calculate_expression_similarity_transcript}}.
#' @param names whether to output names (default) or characterisation
#' as similarity or dissimilarity (used internally to invert dissimilarity measures)
#' @return A character vector of options for the method arguement of the similarity calculation;
#' if names=FALSE, a vector of types (similarity/dissimilarity measure) of the same length
#' @export
#' @examples get_methods_correlation_distance()
get_methods_correlation_distance = function(names=TRUE){
if(names){
methods.correlation <- base::c("pearson", "kendall", "spearman")
methods.distance <- philentropy::getDistMethods()
methods.all <- base::c(base::paste0("correlation_", methods.correlation),
base::paste0("distance_", methods.distance))
return(methods.all)
}else{
is.similarity <- base::c(1, 1, 1, # correlations
0, 0, 0, 0, # Lp Minkowski Family
0, 0, 0, 0, 0, 0, # L1 Family
1, 0, 0, 0, 0, 0, 0, 1, # Intersection Family
1, 1, 1, 1, 0, 0, # Inner Product Family
1, 0, 0, 0, 0, # Squared-chord Family
0, 0, 0, 0, 0, 0, 0, 0, # Squared L2 family (X2 squared family)
0, 0, 0, 0, 0, 0, # Shannon’s Entropy Family
0, 0, 0 # Combinations
)
types.all <- base::rep("d", length(is.similarity))
types.all[is.similarity == 1] <- "s"
return(types.all)
}
}
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