R/collapseRowsUsingKME.R

In milescsmith/WGCNA: Weighted Correlation Network Analysis

# This function chooses a single plobe per gene based on a kME table
collapseRowsUsingKME <- function(MM, Gin, Pin = NULL, kMEcols = 1:dim(MM)[2]) {
  if (is.null(Pin)) Pin <- rownames(MM)
  rownames(MM) <- Pin
  Gout <- as.character(sort(unique(Gin)))
  cors <- MM[, kMEcols]
  maxC <- apply(cors, 1, max)

  MMout <- matrix(0, nrow = length(Gout), ncol = dim(MM)[2])
  colnames(MMout) <- colnames(MM)
  rownames(MMout) <- Gout
  MM <- as.matrix(MM)

  keepThese <- NULL
  for (g in 1:length(Gout)) {
    maxCg <- maxC
    maxCg[Gin != Gout[g]] <- -1000
    keep <- which(maxCg == max(maxCg))[1]
    MMout[g, ] <- MM[keep, ]
    keepThese <- c(keepThese, keep)
  }
  group2Row <- cbind(Gout, Pin[keepThese])
  colnames(group2Row) <- c("group", "selectedRowID")
  selectedRow <- is.element(1:length(Pin), keepThese)
  out <- list(MMout, group2Row, selectedRow)
  names(out) <- c("MMcollapsed", "group2Row", "selectedRow")
  return(out)
}