fix message info genes counts bellow_threshold

Former-commit-id: 2ed2a843ffdbbbfa3ec776f680b64d984d2820bb
Former-commit-id: 6b71038e295cdf928de3c50bbf20f662b6a08e86
Former-commit-id: 8b0724d579460dbe992e11c6fba60a693d77da75

R/mock_rnaseq.R

@@ -80,7 +80,7 @@ get_messages_sequencing_depth <- function(scaling_factors, threshold_cov_var = 1
 warning_too_low_mu_ij_row <- function(mu_ij_matrix, threshold = 1 ){
   n_too_low_row <- length(which(detect_row_matx_bellow_threshold(mu_ij_matrix, threshold)))
   if (n_too_low_row > 0){
-    msg <- paste("INFO:", n_too_low_row, "genes have all(mu_ij) < 1, indicating very low counts. Consider removing them for future analysis using prepareData2fit with row_cnt_threshold = 10. To detect them, try increasing sequencing depth.\n", 
+    msg <- paste("INFO:", n_too_low_row, "genes have all(mu_ij) < 1, indicating very low counts. Consider removing them for future analysis using prepareData2fit with row_threshold = 10. To detect them in future experiment, try increasing sequencing depth.\n", 
                  sep = " ")
     message(msg)
   }

R/prepare_data2fit.R

@@ -147,7 +147,7 @@ prepareData2fit <- function(countMatrix, metadata, response_name = "kij",
   if (row_threshold > 0){          
       message(paste("INFO: filtering", response_name, "<", row_threshold, sep = " " ))
       idx <- detect_row_matx_bellow_threshold(countMatrix, threshold = row_threshold)
-      message(paste(length(idx), "genes removed from data.", sep = " "))
+      message(paste(length(which(idx)), "genes removed from data.", sep = " "))
       countMatrix <- countMatrix[ !idx , ]
   }
   

R/utils.R

@@ -54,7 +54,7 @@ first_non_null_index <- function(lst) {
 #' @return A logical vector indicating rows below the threshold
 #' @export
 detect_row_matx_bellow_threshold <- function(matrix, threshold) {
-             apply(matrix, 1, function(row) all(row < threshold))
+    apply(matrix, 1, function(row) all(row < threshold))
 }