R/compute_CYT.R

In olapuentesantana/easier: Estimate Systems Immune Response from RNA-seq data

#' Compute cytolytic activity (CYT) score
#'
#' Calculates the CYT score using the geometric mean of its
#' signature genes, as defined in Rooney et al., Cell, 2015.
#'
#' @references Rooney, M.S., Shukla, S.A., Wu, C.J., Getz, G.,
#' and Hacohen, N. (2015). Molecular and genetic properties
#' of tumors associated with local immune cytolytic activity.
#' Cell 160, 48–61. https://doi.org/10.1016/j.cell.2014.12.033.
#'
#' @param matches numeric vector indicating the index of signature
#' genes in `RNA_tpm`.
#' @param RNA_tpm data.frame containing TPM values with HGNC symbols
#' in rows and samples in columns.
#'
#' @return A numeric matrix with samples in rows and CTY score
#' in a column.
#'
compute_CYT <- function(matches, RNA_tpm) {
  # Subset RNA_tpm
  subset_RNA_tpm <- RNA_tpm[matches, ]

  # Calculation: geometric mean (so-called log-average)
  #  [TPM, 0.01 offset]
  score <- as.matrix(apply(
    subset_RNA_tpm + 0.01, 2,
    function(X) exp(mean(log(X)))
  ))

  return(data.frame(CYT = score, check.names = FALSE))
}