Try to solve the variableMetadata column problem v2

workflow4metabolomics · Nov 5, 2024 · 04a9bdd · 04a9bdd
1 parent dd106f1
commit 04a9bdd
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Showing 4 changed files with 16 additions and 8 deletions.
diff --git a/tools/camera/CAMERA_findAdducts.R b/tools/camera/CAMERA_findAdducts.R
@@ -125,16 +125,18 @@ ncols <- length(colnames(peakList))
 sample_cols <- length(rownames(xdata@phenoData)) # Number of samples
 
 # Indices for the columns of interest
-main_cols <- 1:(ncols - sample_cols) # Main columns before sample columns
+main_cols <- 1:(ncols - sample_cols - 3) # Main columns before sample columns
 tail_cols <- (ncols - 2):ncols # The last 3 columns (adduct, isotope, pcgroup)
 
 # Combine the selected columns from matgrp with the group names
 variableMetadata <- cbind(
   name = names_default,
   name_custom = names_custom,
-  peakList[, c(main_cols, tail_cols)]
+  stringsAsFactors = FALSE
 )
 
+variableMetadata <- cbind(variableMetadata, peakList[, c(main_cols, tail_cols)])
+
 if (!exists("RTinMinute")) RTinMinute <- FALSE
 
 if (args$convertRTMinute && RTinMinute == FALSE) {

diff --git a/tools/camera/CAMERA_findIsotopes.R b/tools/camera/CAMERA_findIsotopes.R
@@ -112,16 +112,18 @@ ncols <- length(colnames(peakList))
 sample_cols <- length(rownames(xdata@phenoData)) # Number of samples
 
 # Indices for the columns of interest
-main_cols <- 1:(ncols - sample_cols) # Main columns before sample columns
+main_cols <- 1:(ncols - sample_cols - 3) # Main columns before sample columns
 tail_cols <- (ncols - 2):ncols # The last 3 columns (adduct, isotope, pcgroup)
 
 # Combine the selected columns from matgrp with the group names
 variableMetadata <- cbind(
   name = names_default,
   name_custom = names_custom,
-  peakList[, c(main_cols, tail_cols)]
+  stringsAsFactors = FALSE
 )
 
+variableMetadata <- cbind(variableMetadata, peakList[, c(main_cols, tail_cols)])
+
 if (!exists("RTinMinute")) RTinMinute <- FALSE
 
 if (args$convertRTMinute && RTinMinute == FALSE) {

diff --git a/tools/camera/CAMERA_groupCorr.R b/tools/camera/CAMERA_groupCorr.R
@@ -84,16 +84,18 @@ ncols <- length(colnames(peakList))
 sample_cols <- length(rownames(xdata@phenoData)) # Number of samples
 
 # Indices for the columns of interest
-main_cols <- 1:(ncols - sample_cols) # Main columns before sample columns
+main_cols <- 1:(ncols - sample_cols - 3) # Main columns before sample columns
 tail_cols <- (ncols - 2):ncols # The last 3 columns (adduct, isotope, pcgroup)
 
 # Combine the selected columns from matgrp with the group names
 variableMetadata <- cbind(
   name = names_default,
   name_custom = names_custom,
-  peakList[, c(main_cols, tail_cols)]
+  stringsAsFactors = FALSE
 )
 
+variableMetadata <- cbind(variableMetadata, peakList[, c(main_cols, tail_cols)])
+
 if (!exists("RTinMinute")) RTinMinute <- FALSE
 
 if (args$convertRTMinute == TRUE && RTinMinute == FALSE) {

diff --git a/tools/camera/CAMERA_groupFWHM.R b/tools/camera/CAMERA_groupFWHM.R
@@ -87,16 +87,18 @@ ncols <- length(colnames(peakList))
 sample_cols <- length(rownames(xdata@phenoData)) # Number of samples
 
 # Indices for the columns of interest
-main_cols <- 1:(ncols - sample_cols) # Main columns before sample columns
+main_cols <- 1:(ncols - sample_cols - 3) # Main columns before sample columns
 tail_cols <- (ncols - 2):ncols # The last 3 columns (adduct, isotope, pcgroup)
 
 # Combine the selected columns from matgrp with the group names
 variableMetadata <- cbind(
   name = names_default,
   name_custom = names_custom,
-  peakList[, c(main_cols, tail_cols)]
+  stringsAsFactors = FALSE
 )
 
+variableMetadata <- cbind(variableMetadata, peakList[, c(main_cols, tail_cols)])
+
 if (!exists("RTinMinute")) RTinMinute <- FALSE
 
 if (args$convertRTMinute && RTinMinute == FALSE) {