R/get.konecny.subtypes.R

In bhklab/consensusOV: Gene expression-based subtype classification for high-grade serous ovarian cancer

#' Get ovarian cancer subtypes as defined by Konecny et al., 2014
#'
#' @param expression.matrix A matrix of gene expression values with rows as
#' genes, columns as samples.
#' @param entrez.ids A vector of Entrez Gene IDs, corresponding to the rows of
#' \code{expression.matrix}
#' @return A list with first value \code{Konecny.subtypes} containing a factor
#' of subtype names; and second value \code{spearman.cc.vals} containing the
#' Spearman correlation values per subtype
#' @examples
#' library(Biobase)
#' data(GSE14764.eset)
#' expression.matrix <- exprs(GSE14764.eset)
#' entrez.ids <- as.character(fData(GSE14764.eset)$EntrezGene.ID)
#' get.konecny.subtypes(expression.matrix, entrez.ids)
#' @references Konecny et al. \emph{Prognostic and therapeutic relevance of
#' molecular subtypes in high-grade serous ovarian cancer.}
#' Journal of the National Cancer Institute (2014).
#' @export
get.konecny.subtypes <-
function(expression.matrix, entrez.ids) {

  expression.matrix <- t(scale(t(expression.matrix)))
  entrez.ids <- as.character(entrez.ids)
  ## Classify using nearest centroid with Spearman's rho
  intersecting.entrez.ids <- intersect(entrez.ids, rownames(konecny.centroids))

  konecny.centroids[rownames(konecny.centroids) %in% intersecting.entrez.ids,]
  konecny.centroids <- konecny.centroids[as.character(intersecting.entrez.ids),]
  expression.matrix <- expression.matrix[entrez.ids %in% intersecting.entrez.ids,]

  expression.matrix <- as.data.frame(expression.matrix)
  spearman.cc.vals <- sapply(
      konecny.centroids,
      function(x) sapply(expression.matrix,
                         function(y) cor(x, y , method="spearman")))

  ind <- apply(spearman.cc.vals, 1, which.max)
  subclasses <- colnames(spearman.cc.vals)[ind]
  subclasses <- factor(subclasses, levels=colnames(konecny.centroids))

  return(list(Konecny.subtypes=subclasses, spearman.cc.vals=spearman.cc.vals))
}