add rm.zero option

R/pgx-functions.R

@@ -2284,6 +2284,8 @@ make_unique <- function(s, sep = "") {
   s
 }
 
+#' Check if values are logarithm
+#' 
 #' @export
 is_logged <- function(x, verbose = 0) {
   ## force as matrix

R/pgx-normalize.R

@@ -175,16 +175,19 @@ NORMALIZATION.METHODS <- c("none", "mean.center", "median.center", "sum", "CPM",
 #' normalized <- pgx.countNormalization(counts, c("TMM", "RLE"))
 #' }
 #' @export
-pgx.countNormalization <- function(x, methods, ref = NULL) {
+pgx.countNormalization <- function(x, methods, ref = NULL, rm.zero=FALSE) {
   ## Column-wise normalization (along samples).
   ## x:        counts (linear)
   ## method:   single method
 
   methods <- methods[1]
-  ## which.zero <- which(x == 0, arr.ind = TRUE)
-  ## x1 <- x
-  ## x1[which.zero] <- NA
-
+
+  if(rm.zero) {
+    minx <- min(x,na.rm = TRUE)
+    which.zero <- which(x == minx, arr.ind = TRUE)
+    x[which.zero] <- NA
+  }
+
   for (m in methods) {
     if (m == "none") {
       x <- x
@@ -227,8 +230,10 @@ pgx.countNormalization <- function(x, methods, ref = NULL) {
     }
   }
 
-  ## put back zeros as zeros
-  ## x[which.zero] <- 0
+  if(rm.zero) {
+    ## put back zeros as zeros
+    x[which.zero] <- minx
+  }
   return(x)
 }