R/adjacency.polyReg.R

In milescsmith/WGCNA: Weighted Correlation Network Analysis

adjacency.polyReg <- function(datExpr, degree = 3, symmetrizationMethod = "mean") {
  if (!is.element(symmetrizationMethod, c("none", "min", "max", "mean"))) {
    stop("Unrecognized symmetrization method.")
  }

  datExpr <- matrix(as.numeric(as.matrix(datExpr)), nrow(datExpr), ncol(datExpr))
  n <- ncol(datExpr)
  polyRsquare <- matrix(NA, n, n)

  for (i in 2:n) {
    for (j in 1:(i - 1)) {
      del <- is.na(datExpr[, i] + datExpr[, j])
      if (sum(del) >= (n - 1) | var(datExpr[, i], na.rm = T) == 0 | var(datExpr[, j], na.rm = T) == 0) {
        polyRsquare[i, j] <- polyRsquare[j, i] <- NA
      } else {
        dati <- datExpr[!del, i]
        datj <- datExpr[!del, j]
        lmPij <- glm(dati ~ poly(datj, degree))
        polyRsquare[i, j] <- cor(dati, predict(lmPij))^2
        lmPji <- glm(datj ~ poly(dati, degree))
        polyRsquare[j, i] <- cor(datj, predict(lmPji))^2
        rm(dati, datj, lmPij, lmPji)
      }
    }
  }

  diag(polyRsquare) <- rep(1, n)

  if (symmetrizationMethod == "none") {
    adj <- polyRsquare
  } else {
    adj <- switch(symmetrizationMethod,
      min = pmin(polyRsquare, t(polyRsquare)),
      max = pmax(polyRsquare, t(polyRsquare)),
      mean = (polyRsquare + t(polyRsquare)) / 2
    )
  }
  adj
}