fix quotes in NAMESPACE

ipb-halle · Jan 30, 2025 · 0a349b9 · 0a349b9
2 parents 211b2f6 + b678591
commit 0a349b9
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Showing 4 changed files with 12 additions and 10 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -36,6 +36,6 @@ importFrom("stats", "as.dendrogram", "cor", "dendrapply", "dist",
 importFrom("utils", "flush.console", "read.table")
 
 
-importFrom("SummarizedExperiment","colData")
-importFrom("SummarizedExperiment","rowData", "rowData<-")
-importFrom("SummarizedExperiment","assay")
+importFrom(SummarizedExperiment,colData)
+importFrom("SummarizedExperiment","rowData","rowData<-")
+importFrom(SummarizedExperiment,assay)
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]])
@@ -194,6 +194,7 @@ parsePeakAbundanceMatrixQF <- function(qfeatures,
 #' @importFrom SummarizedExperiment rowData
 #' @importFrom SummarizedExperiment rowData<- 
 #' @export
+#' @importFrom SummarizedExperiment rowData<-
 #'
 #' @examples
 addSiriusAnnotations <- function(qfeatures,

diff --git a/vignettes/discoveringregulatedmetabolitefamilies.Rmd b/vignettes/discoveringregulatedmetabolitefamilies.Rmd
@@ -97,7 +97,7 @@ pcaDimensionTwo <<- 2
 
   resultObj <- calcPlotPCAscores(
     pcaObj = pca, 
-    dataList = project, 
+    dataList = dataList, #project, 
     filterObj = filterObj,
     pcaDimensionOne = pcaDimensionOne, 
     pcaDimensionTwo = pcaDimensionTwo, 
@@ -108,7 +108,7 @@ pcaDimensionTwo <<- 2
 
   resultObj <- calcPlotPCAloadings(
     pcaObj = pca, 
-    dataList = project, 
+    dataList = dataList, #project, 
     filter = filterObj, 
     pcaDimensionOne = pcaDimensionOne, 
     pcaDimensionTwo = pcaDimensionTwo, 
@@ -136,9 +136,9 @@ HCA on MS2 in Figure \@ref(fig:hca).
 ```{r hca, fig.cap="HCA on MS2.", echo=FALSE}
 
 if (FALSE) {
-p <- calcPlotDendrogram_plotly(dataList=project, 
+p <- calcPlotDendrogram_plotly(dataList=dataList, #project, 
                                filterObj=filterObj, 
-                               clusterDataList=project, 
+                               clusterDataList=dataList, #project, 
   distanceMeasure = "Jaccard", 
   showClusterLabels=FALSE, 
   hcaPrecursorLabels="m/z / RT", 
@@ -156,7 +156,7 @@ load(fileName)
 fileName <- system.file("extdata/testdata/hcaFilter.Rdata", package = "MetFamily")
 load(fileName) 
 
-returnObj <- calcPlotDendrogram(dataList=project, 
+returnObj <- calcPlotDendrogram(dataList=dataList, #project, 
                                 filter=filter, 
                                 clusterDataList=clusterDataList, 
                                 annoPresentAnnotationsList = annoPresentAnnotationsList ,