fix: phenoData

workflow4metabolomics · Nov 5, 2024 · b16ecf1 · b16ecf1
1 parent 96d4228
commit b16ecf1
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Showing 4 changed files with 8 additions and 7 deletions.
diff --git a/tools/camera/CAMERA_findAdducts.R b/tools/camera/CAMERA_findAdducts.R
@@ -122,7 +122,7 @@ names_custom <- groupnames(xa@xcmsSet, mzdec = args$numDigitsMZ, rtdec = args$nu
 # Calculate indices of the columns to include from peakList
 # Select all columns except the last sample-specific columns
 ncols <- length(colnames(peakList))
-sample_cols <- length(rownames(xdata@phenoData)) # Number of samples
+sample_cols <- length(rownames(phenoData)) # Number of samples
 
 # Indices for the columns of interest
 main_cols <- 1:(ncols - sample_cols - 3) # Main columns before sample columns
@@ -150,7 +150,7 @@ write.table(variableMetadata, file = output_file_tsv, sep = "\t", row.names = FA
 
 # Save the updated xsAnnotate object
 output_file_RData <- "camera_findAdducts.RData"
-objects2save <- c("xa", "variableMetadata", "listOFlistArguments", "zipfile", "singlefile", "RTinMinute", "xdata@phenoData")
+objects2save <- c("xa", "variableMetadata", "listOFlistArguments", "zipfile", "singlefile", "RTinMinute", "phenoData")
 save(list = objects2save[objects2save %in% ls()], file = output_file_RData)
 
 cat("Output files generated:", output_file_tsv, "and", output_file_RData, "\n")
diff --git a/tools/camera/CAMERA_findIsotopes.R b/tools/camera/CAMERA_findIsotopes.R
@@ -109,7 +109,7 @@ names_custom <- groupnames(xa@xcmsSet, mzdec = args$numDigitsMZ, rtdec = args$nu
 # Calculate indices of the columns to include from peakList
 # Select all columns except the last sample-specific columns
 ncols <- length(colnames(peakList))
-sample_cols <- length(rownames(xdata@phenoData)) # Number of samples
+sample_cols <- length(rownames(phenoData)) # Number of samples
 
 # Indices for the columns of interest
 main_cols <- 1:(ncols - sample_cols - 3) # Main columns before sample columns
@@ -138,7 +138,7 @@ write.table(variableMetadata, file = output_file_tsv, sep = "\t", row.names = FA
 # Save the updated xsAnnotate object
 output_file_RData <- "camera_findIsotopes.RData"
 
-objects2save <- c("xa", "variableMetadata", "listOFlistArguments", "zipfile", "singlefile", "RTinMinute", "xdata@phenoData")
+objects2save <- c("xa", "variableMetadata", "listOFlistArguments", "zipfile", "singlefile", "RTinMinute", "phenoData")
 save(list = objects2save[objects2save %in% ls()], file = output_file_RData)
 
 cat("Output files generated:", output_file_tsv, "and", output_file_RData, "\n")
diff --git a/tools/camera/CAMERA_groupCorr.R b/tools/camera/CAMERA_groupCorr.R
@@ -81,7 +81,7 @@ names_custom <- groupnames(xa@xcmsSet, mzdec = args$numDigitsMZ, rtdec = args$nu
 # Calculate indices of the columns to include from peakList
 # Select all columns except the last sample-specific columns
 ncols <- length(colnames(peakList))
-sample_cols <- length(rownames(xdata@phenoData)) # Number of samples
+sample_cols <- length(rownames(phenoData)) # Number of samples
 
 # Indices for the columns of interest
 main_cols <- 1:(ncols - sample_cols - 3) # Main columns before sample columns
@@ -109,7 +109,7 @@ write.table(variableMetadata, file = output_file_tsv, sep = "\t", row.names = FA
 
 # Save the updated xsAnnotate object
 output_file_RData <- "camera_groupCorr.RData"
-objects2save <- c("xa", "variableMetadata", "listOFlistArguments", "zipfile", "singlefile", "RTinMinute", "xdata@phenoData")
+objects2save <- c("xa", "variableMetadata", "listOFlistArguments", "zipfile", "singlefile", "RTinMinute", "phenoData")
 save(list = objects2save[objects2save %in% ls()], file = output_file_RData)
 
 cat("Output files generated:", output_file_tsv, "and", output_file_RData, "\n")
diff --git a/tools/camera/CAMERA_groupFWHM.R b/tools/camera/CAMERA_groupFWHM.R
@@ -71,6 +71,7 @@ if (!is.null(singlefile)) {
 
 # If the xdata object exists, convert it to xcmsSet
 if (exists("xdata")) {
+  phenoData <- xdata@phenoData
   xset <- getxcmsSetObject(xdata)
 }
 
@@ -125,7 +126,7 @@ write.table(variableMetadata, file = output_file_tsv, sep = "\t", row.names = FA
 
 # Save the xsAnnotate object
 output_file_RData <- "camera_fwhm.RData"
-objects2save <- c("xa", "variableMetadata", "listOFlistArguments", "zipfile", "singlefile", "RTinMinute", "xdata@phenoData")
+objects2save <- c("xa", "variableMetadata", "listOFlistArguments", "zipfile", "singlefile", "RTinMinute", "phenoData")
 save(list = objects2save[objects2save %in% ls()], file = output_file_RData)
 
 cat("Output files generated:", output_file_tsv, "and", output_file_RData, "\n")