warning on nas in prediction, error in test (openproblems-bio#54)

Paulos2411 · May 30, 2024 · a90f631 · a90f631
1 parent 7404b19
commit a90f631
Show file tree

Hide file tree

Showing 3 changed files with 18 additions and 1 deletion.
diff --git a/src/task/metrics/mean_correlation_r/script.R b/src/task/metrics/mean_correlation_r/script.R
@@ -30,6 +30,14 @@ prediction <- prediction[, genes]
 de_test_X <- de_test$layers[[par$de_test_layer]]
 prediction_X <- prediction$layers[[par$prediction_layer]]
 
+if (any(is.na(de_test_X))) {
+  stop("NA values in de_test_X")
+}
+if (any(is.na(prediction_X))) {
+  warning("NA values in prediction_X")
+  prediction_X[is.na(prediction_X)] <- 0
+}
+
 cat("Calculate metrics\n")
 out <- cor(t(de_test_X), t(prediction_X), method = "pearson")
 pearson <- diag(out)

diff --git a/src/task/metrics/mean_cosine_sim_r/script.R b/src/task/metrics/mean_cosine_sim_r/script.R
@@ -30,6 +30,14 @@ prediction <- prediction[, genes]
 de_test_X <- de_test$layers[[par$de_test_layer]]
 prediction_X <- prediction$layers[[par$prediction_layer]]
 
+if (any(is.na(de_test_X))) {
+  stop("NA values in de_test_X")
+}
+if (any(is.na(prediction_X))) {
+  warning("NA values in prediction_X")
+  prediction_X[is.na(prediction_X)] <- 0
+}
+
 cat("Clipping values\n")
 threshold_0001 <- -log10(0.0001)
 de_test_X_clipped_0001 <- pmax(pmin(de_test_X, threshold_0001), -threshold_0001)

diff --git a/src/task/metrics/mean_rowwise_error_r/script.R b/src/task/metrics/mean_rowwise_error_r/script.R
@@ -34,7 +34,8 @@ if (any(is.na(de_test_X))) {
   stop("NA values in de_test_X")
 }
 if (any(is.na(prediction_X))) {
-  stop("NA values in prediction_X")
+  warning("NA values in prediction_X")
+  prediction_X[is.na(prediction_X)] <- 0
 }
 
 cat("Clipping values\n")