R/compute_chemokines.R

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

#' Compute chemokine signature (chemokines) score
#'
#' Calculates chemokines score as the PC1 score that results
#' from applying PCA to the expression of its signature genes,
#' defined in Messina et al., Sci. Rep., 2012.
#'
#' @references Messina, J.L., Fenstermacher, D.A., Eschrich, S.,
#' Qu, X., Berglund, A.E., Lloyd, M.C., Schell, M.J., Sondak, V.K.,
#' Weber, J.S., and Mule, J.J. (2012). 12-Chemokine gene signature
#' identifies lymph node-like structures in melanoma: potential for
#' patient selection for immunotherapy? Sci. Rep. 2, 765.
#' https://doi.org/10.1038/srep00765.
#'
#' @importFrom stats prcomp
#'
#' @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 chemokines
#' score in a column.
#'
compute_chemokines <- function(matches, RNA_tpm) {
  # Log2 transformation:
  log2_RNA_tpm <- log2(RNA_tpm + 1)

  # Subset gene_expr
  sub_log2_RNA_tpm <- log2_RNA_tpm[matches, ]

  # calculation: using PCA (Z-score calculated within prcomp)
  chemokine_pca <- stats::prcomp(t(sub_log2_RNA_tpm),
    center = TRUE, scale = TRUE
  )
  score <- chemokine_pca$x[, 1]

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