R/CPD.R

In DavisLaboratory/msImpute: Imputation of label-free mass spectrometry peptides

#' CPD
#'
#' Spearman correlation between pairwise distances in the original data and imputed data.
#' CPD quantifies preservation of the global structure after imputation.
#' Requires complete datasets - for developers/use in benchmark studies only.
#'
#' @param xorigin numeric matrix. The original log-intensity data. Can not contain missing values.
#' @param ximputed numeric matrix. The imputed log-intensity data. Can not contain missing values.
#'
#' @return numeric
#' @examples
#' data(pxd007959)
#' y <- pxd007959$y
#' y <- y[complete.cases(y),]
#' # for demonstration we use same y for xorigin and ximputed
#' CPD(y, y)
#'
#' @importFrom stats cor dist
#' @export
CPD <- function(xorigin, ximputed){
  return(cor(x=as.numeric(dist(t(xorigin))),
             y = as.numeric(dist(t(ximputed))),
             method = "spearman"))
}