From e9a15a2e992fdecbd8c660b11ca312530ff7c267 Mon Sep 17 00:00:00 2001 From: Christina Schmidt Date: Wed, 19 Feb 2025 09:15:10 +0100 Subject: [PATCH] Bug fix for blanks =2 in CoRe= TRUE as empty DF was returned and caused error in saving. --- R/Processing.R | 11 ++++++++++- vignettes/CoRe Metabolomics.Rmd | 6 +++--- 2 files changed, 13 insertions(+), 4 deletions(-) diff --git a/R/Processing.R b/R/Processing.R index 5df3bc2..9935a10 100644 --- 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 index b01b08a..492fc26 100644 --- 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