Bug fix for blanks =2 in CoRe= TRUE as empty DF was returned and caus…

…ed error in saving.
saezlab · Feb 19, 2025 · e9a15a2 · e9a15a2
1 parent 5ea4024
commit e9a15a2
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Showing 2 changed files with 13 additions and 4 deletions.
diff --git a/R/Processing.R b/R/Processing.R
@@ -213,7 +213,11 @@ PreProcessing <- function(InputData,
   }
 
   if(CoRe ==TRUE){
-     DFList_CoRe <- list( "CV_CoRe_blank"= data_CoReNorm[["DF"]][["CV_CoRe_blank"]],"Variation_ContigencyTable_CoRe_blank"=data_CoReNorm[["DF"]][["Contigency_table_CoRe_blank"]])
+    if(is.null(data_CoReNorm[["DF"]][["Contigency_table_CoRe_blank"]])){
+      DFList_CoRe <- list( "CV_CoRe_blank"= data_CoReNorm[["DF"]][["CV_CoRe_blank"]])
+    }else{
+      DFList_CoRe <- list( "CV_CoRe_blank"= data_CoReNorm[["DF"]][["CV_CoRe_blank"]],"Variation_ContigencyTable_CoRe_blank"=data_CoReNorm[["DF"]][["Contigency_table_CoRe_blank"]])
+    }
      DFList <- c(DFList, DFList_CoRe)
   }
 
@@ -1177,6 +1181,11 @@ CoReNorm <-function(InputData,
       }
       # Filter the CoRe_media samples
       CoRe_medias <- CoRe_medias %>% dplyr::filter(!rownames(CoRe_medias) %in% different_samples)
+    }else{
+      message <- paste0("Only >=2 blank samples available. Thus,we can not perform outlier testing for the blank samples.")
+      logger::log_trace(message)
+      message(message)
+
     }
     CoRe_media_df <- as.data.frame(data.frame("CoRe_mediaMeans"=  colMeans(CoRe_medias, na.rm = TRUE)))
   }

diff --git a/vignettes/CoRe Metabolomics.Rmd b/vignettes/CoRe Metabolomics.Rmd
@@ -195,9 +195,9 @@ Media_Metadata <- Media%>%
 PreProcessing_res <-  MetaProViz::PreProcessing(InputData=Media_input,
                                                 SettingsFile_Sample =Media_Metadata,
                                                 SettingsInfo = c(Conditions = "Conditions",
-                                                                       Biological_Replicates = "Biological_Replicates",
-                                                                       CoRe_norm_factor = "GrowthFactor",
-                                                                       CoRe_media = "blank"),
+                                                                 Biological_Replicates = "Biological_Replicates",
+                                                                 CoRe_norm_factor = "GrowthFactor",
+                                                                 CoRe_media = "blank"),
                                                 FeatureFilt = "Modified",
                                                 FeatureFilt_Value = 0.8,
                                                 TIC = TRUE,# As we have raw data we will perform total ion count norm