fix hca and other warning

ipb-halle · Nov 12, 2024 · 4e82129 · 4e82129
1 parent 262bb3f
commit 4e82129
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/R/DataProcessing.R b/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

diff --git a/R/parsePeakAbundanceMatrixQF.R b/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]])