fix xgboost label as logical in scoreReadClass and junction site prediction

Chen Ying · Chen Ying · commit a7599cfabeb3 · 2026-01-09T10:16:59.000+08:00
diff --git a/R/bambu-processReads_scoreReadClasses.R b/R/bambu-processReads_scoreReadClasses.R
@@ -294,6 +294,7 @@ prepareTranscriptModelFeatures = function(rowData){
                       tx_strand_bias = readCount.posStrand, labels = equal) %>%
         mutate(
             tx_strand_bias=(1-abs(0.5-(tx_strand_bias/numReads))),
+			labels = as.logical(labels),
             numReads = log2(pmax(1,1+(numReads/scalingFactor)))
         )
     return(outData)
diff --git a/R/bambu-processReads_utilityJunctionErrorCorrection.R b/R/bambu-processReads_utilityJunctionErrorCorrection.R
@@ -92,7 +92,7 @@ testSpliceSites <- function(data, splice = "Start", prime = "start",
         predSplice.prime <- NULL
         if (is.null(junctionModel)) { 
             model = fitXGBoostModel(labels.train = 
-                as.integer(annotatedSplice)[mySet.all][mySet.training], 
+                as.logical(annotatedSplice)[mySet.all][mySet.training], 
                 data.train = modelmatrix[mySet.training,],
                 show.cv = verbose, maxSize.cv = 10000)
             

Original file line number	Diff line number	Diff line change
`@@ -294,6 +294,7 @@ prepareTranscriptModelFeatures = function(rowData){`
`294`	`294`	`tx_strand_bias = readCount.posStrand, labels = equal) %>%`
`295`	`295`	`mutate(`
`296`	`296`	`tx_strand_bias=(1-abs(0.5-(tx_strand_bias/numReads))),`
	`297`	`+ labels = as.logical(labels),`
`297`	`298`	`numReads = log2(pmax(1,1+(numReads/scalingFactor)))`
`298`	`299`	`)`
`299`	`300`	`return(outData)`