fix hca and other warning

Author: NorStorz

R/DataProcessing.R

@@ -1440,7 +1440,8 @@ getMS2spectrumInfoForCluster <- function(dataList, clusterDataList, treeLabel){
   #fragmentsX <- dataList$fragmentMasses[featuresIntersection]
   #fragmentsY <- apply(X = data.numericmatrix(dataList$featureMatrix[clusterMembersPrecursors, featuresIntersection]), MARGIN = 2, FUN = mean)
   fragmentsX <- dataList$fragmentMasses[featuresUnion]
-  fragmentsY <- apply(X = data.numericmatrix(dataList$featureMatrix[clusterMembersPrecursors, featuresUnion]), MARGIN = 2, FUN = mean)
+  #fragmentsY <- apply(X = data.numericmatrix(dataList$featureMatrix[clusterMembersPrecursors, featuresUnion]), MARGIN = 2, FUN = mean)
+  fragmentsY <- apply( X = data.matrix(dataList$featureMatrix[clusterMembersPrecursors, featuresUnion, drop = FALSE]), MARGIN = 2, FUN = mean )
 
   selectedPositive <- clusterDataList$innerNodeFeaturesCountsMatrix[clusterIndex, featuresUnion]
   coverageSelected <- selectedPositive / numberOfClusterMembers

R/parsePeakAbundanceMatrixQF.R

@@ -40,7 +40,7 @@ parsePeakAbundanceMatrixQF <- function(qfeatures,
   dataFrame <- cbind(rowData(qfeatures)[[1]][,cols_to_keep] ,assay(qfeatures))
   #workaround for avoiding change in colnames during coercion
   cnames <- colnames(dataFrame)
-  dataFrame <- as.data.frame(dataFrame, check.names = FALSE)
+  dataFrame <- as.data.frame(dataFrame)
   colnames(dataFrame) <- cnames
   oldFormat <- ncol(colData(qfeatures))==3
   numRowDataCols <- ncol(rowData(qfeatures)[[1]])