merging sirius annotation

ipb-halle · Sep 19, 2024 · 2c72f7b · 2c72f7b
1 parent b6eaf84
commit 2c72f7b
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Showing 2 changed files with 11 additions and 33 deletions.
diff --git a/R/FragmentMatrixFunctions.R b/R/FragmentMatrixFunctions.R
@@ -1438,6 +1438,7 @@ convertToProjectFile <- function(filePeakMatrixPath,
 
   filePeakMatrixQF <- readMSDial(filePeakMatrixPath)
   if (!is.null(fileAnnotation)){
+    # TODO: determine colums to merge by
     addSiriusAnnotations(filePeakMatrixQF,fileAnnotation)
   }
 
@@ -1593,7 +1594,7 @@ convertToProjectFile2 <- function(filePeakMatrixQF,
   #temporary fix
   #filePeakMatrix <- NULL
 
-  if(!is.null(filePeakMatrix)){
+  if(!is.null(filePeakMatrixQF)){
     ## allHits: dataFrame$"Average Mz" --> precursorMz; allHits indexes the spectraList
     diffAll <- abs(outer(X = precursorMz, Y = dataFrame$"Average Mz", FUN = function(x, y){abs(x-y)}))
     allHits <- apply(X = diffAll, MARGIN = 2, FUN = function(x){which(x == min(x[x < parameterSet$mzDeviationAbsolute_mapping], Inf))})

diff --git a/R/parsePeakAbundanceMatrixQF.R b/R/parsePeakAbundanceMatrixQF.R
@@ -42,7 +42,7 @@ parsePeakAbundanceMatrixQF <- function(qfeatures,
   cnames <- colnames(dataFrame)
   dataFrame <- as.data.frame(dataFrame, check.names = FALSE)
   colnames(dataFrame) <- cnames
-  datoldFormat <- ncol(colData(qfeatures))==3
+  oldFormat <- ncol(colData(qfeatures))==3
   numRowDataCols <- ncol(rowData(qfeatures)[[1]])
   dataColumnStartEndIndeces <- c(numRowDataCols+1,ncol(dataFrame))
   numberOfPrecursors <- nrow(dataFrame)
@@ -180,8 +180,6 @@ parsePeakAbundanceMatrixQF <- function(qfeatures,
   return (returnObj)
 }
 
-#qfeatures <- readMSDial("inst/extdata/showcase/Metabolite_profile_showcase.txt")
-#siriusFile <- "inst/extdata/testdata/canopus/canopusShort.txt"
 #' Title
 #'
 #' @param qfeatures 
@@ -195,39 +193,22 @@ parsePeakAbundanceMatrixQF <- function(qfeatures,
 #' @examples
 addSiriusAnnotations <- function(qfeatures,
                                  siriusFile,
-                                 rowData_col = NULL,
-                                 sirius_col =NULL) {
-
+                                 rowData_col = "Alignment ID",
+                                 sirius_col = "featureId") {
+  #TODO: specify more parameters in read delim
   annotation <- read.delim(siriusFile)
 
   rowData <- rowData(qfeatures[[1]])
 
-  if (is.null(sirius_col)) {
-    sirius_col <- grep("Alignment ID|featureId|ID", colnames(annotation), value = TRUE)
-  }
-
-  if (is.null(rowData_col)) {
-    rowData_col <- grep("featureId|Alignment ID|ID", colnames(rowData), value = TRUE)
-  }
-
-  # Check if the identified columns exist and are unique
-  if (length(sirius_col) != 1) {
-    stop("Could not uniquely identify the annotation column.")
-  }
-  if (length(rowData_col) != 1) {
-    stop("Could not uniquely identify the rowData column.")
-  }
-
   # Print for debugging
   print(paste("Merging by:", sirius_col, "and", rowData_col))
 
   # Merge the data frames
-  annotatedRowData <- merge(annotation, rowData,
-                            by.x = sirius_col, by.y = rowData_col, all.y = TRUE)
- # annotatedRowData <- merge(annotation, rowData, by.x = "Alignment ID", by.y = "featureId", all.y = TRUE)
- #annotatedRowData <- merge(annotation, rowData, by.x = siriusID, by.y =featureID,  all.y = TRUE)
-
-  annotation_cols <- colnames(annotation)[colnames(annotation) != featureID]
+  annotatedRowData <- S4Vectors::merge( rowData, annotation,
+                             by.x = rowData_col, by.y = sirius_col,  all.x = TRUE)
+
+  #TODO: ? check for duplicate columns ?
+  annotation_cols <- colnames(annotation)[colnames(annotation) != rowData_col]
   rowData_cols <- colnames(rowData)
 
   for (col in colnames(annotatedRowData)) {
@@ -237,10 +218,6 @@ addSiriusAnnotations <- function(qfeatures,
       attr(annotatedRowData[[col]], "source") <- "data"
     }
   }
-
-  # Update the row data in qfeatures
   rowData(qfeatures[[1]]) <- annotatedRowData
-
   return(qfeatures)
 }
-#annotation_cols <- names(which(sapply(rowData, function(x) attr(x, "source") == "sirius")))