Merge pull request #521 from GoekeLab/xgboost_x_y_rename_v4

fix xgboost data and label rename to x and y warning

Author: Chen Ying

R/bambu-processReads_utilityJunctionErrorCorrection.R

@@ -211,11 +211,10 @@ fitXGBoostModel <- function(labels.train, data.train, nrounds = 50,
         data.train.cv.test <- data.train[-mySample,]
         labels.train.cv.test <- labels.train[-mySample]
 
-        cv.fit <- xgboost(data = data.train.cv, 
-            label = labels.train.cv, nthread = 1, nrounds = nrounds, 
+        cv.fit <- xgboost(x = data.train.cv, 
+            y = labels.train.cv, nthread = 1, nrounds = nrounds, 
             objective = "binary:logistic", 
-            eval_metric = 'error',
-            verbose = 0)
+            eval_metric = 'error')
         predictions <- predict(cv.fit, data.train.cv.test)
         message('prediction accuracy (CV) (higher for splice ',
                 'donor than splice acceptor)')
@@ -229,11 +228,10 @@ fitXGBoostModel <- function(labels.train, data.train, nrounds = 50,
         message("AUC: ", evaluatePerformance(labels.train.cv.test == 1,predictions)$AUC)
     }
 
-    cv.fit <- xgboost(data = data.train, 
-                      label = labels.train, nthread=1, nrounds=nrounds, 
+    cv.fit <- xgboost(x = data.train, 
+                      y = labels.train, nthread=1, nrounds=nrounds, 
                       objective = "binary:logistic", 
-                      eval_metric='error',
-                      verbose = 0)
+                      eval_metric='error')
 
     return(cv.fit)
 }