return distTable now returns intermediate distTable

GoekeLab · Dec 5, 2024 · 4de8392 · 4de8392
1 parent 22c169c
commit 4de8392
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/R/bambu-assignDist.R b/R/bambu-assignDist.R
@@ -6,7 +6,7 @@ assignReadClasstoTranscripts <- function(readClassList, annotations, isoreParame
                                         verbose, demultiplexed, spatial, 
                                         returnDistTable = FALSE, trackReads = TRUE) {
     if (is.character(readClassList)) readClassList <- readRDS(file = readClassList)
-    metadata(readClassList)$readClassDist <- calculateDistTable(readClassList, annotations, isoreParameters, verbose)
+    metadata(readClassList)$readClassDist <- calculateDistTable(readClassList, annotations, isoreParameters, verbose, returnDistTable)
     readClassList = splitReadClassFiles(readClassList)
     readClassDt <- genEquiRCs(metadata(readClassList)$readClassDist, annotations, verbose) 
     readClassDt$eqClass.match = match(readClassDt$eqClassById,metadata(readClassList)$eqClassById)
@@ -33,7 +33,7 @@ assignReadClasstoTranscripts <- function(readClassList, annotations, isoreParame
     metadata(quantData)$incompatibleCountMatrix  = metadata(readClassList)$incompatibleCountMatrix 
     metadata(quantData)$sampleNames = metadata(readClassList)$sampleNames 
     if(returnDistTable){
-        metadata(quantData)$distTable = metadata(readClassList)$readClassDist
+        metadata(quantData)$distTable = metadata(metadata(readClassList)$readClassDist)$distTableOld
     }
     if (trackReads){
         metadata(quantData)$readToTranscriptMap = 

diff --git a/R/bambu_utilityFunctions.R b/R/bambu_utilityFunctions.R
@@ -225,13 +225,14 @@ handleWarnings <- function(readClassList, verbose){
 }
 
 #' Calculate the dist table used for Bambu Quantification
-calculateDistTable <- function(readClassList, annotations, isoreParameters, verbose){
+calculateDistTable <- function(readClassList, annotations, isoreParameters, verbose, returnDistTable){
     readClassDist <- isore.estimateDistanceToAnnotations(readClassList, annotations,
                                                             min.exonDistance = isoreParameters[["min.exonDistance"]],
                                                             min.primarySecondaryDist = isoreParameters[['min.primarySecondaryDist']],
                                                             min.primarySecondaryDistStartEnd = isoreParameters[['min.primarySecondaryDistStartEnd2']],
                                                             verbose = verbose)
         metadata(readClassDist)$distTable <- modifyIncompatibleAssignment(metadata(readClassDist)$distTable)
+        if(returnDistTable) metadata(readClassDist)$distTableOld = metadata(readClassDist)$distTable
                 #convert string gene ids into index to save memory
         GENEIDs = factor(unique(mcols(annotations)$GENEID))
         GENEID.i = as.numeric(GENEIDs)