pheno data correction column types

mpip · Apr 12, 2024 · 20503d2 · 20503d2
1 parent e2e8455
commit 20503d2
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Showing 2 changed files with 26 additions and 12 deletions.
diff --git a/scripts/10_correction_batch_effects_unfiltered.Rmd b/scripts/10_correction_batch_effects_unfiltered.Rmd
@@ -53,6 +53,13 @@ knitr::opts_chunk$set(echo = FALSE)
 summary_table_preprocessing <- readRDS(paste0(user_choices$project_name, "/reports/summary_table_preprocessing.rds"))
 load(paste0(user_choices$project_name, "/processed_data/Betas_clean_unfiltered_quantile_bmiq.Rdata"))
 load(paste0(user_choices$project_name, "/processed_data/PhenoData_clean.Rdata"))
+phenodata_clean_df <- as.data.frame(PhenoData_clean@listData) %>%
+    dplyr::select(personid, plate, slide, array, row, column, arrayid) %>%
+  mutate(plate = as.factor(plate),
+         slide = as.factor(slide),
+         array = as.factor(array),
+         row = as.factor(row),
+         column = as.factor(column))
 load(paste0(user_choices$project_name, "/processed_data/RGSet_clean.Rdata"))
 phenotype_data <- readRDS(paste0(user_choices$project_name, "/processed_data/phenotype_data.rds"))
 ```
@@ -65,8 +72,8 @@ m_values <- apply(Betas_clean_unfiltered_quantile_bmiq, 2, function(x) log2((x)/
 if (correction_variable_1 == "PLEASE FILL IN"){
   print("No first batch correction variable was specified by user, data remains unchanged")
 } else {
-  mod <- model.matrix(~1, data = PhenoData_clean)
-  m_values_combat_1 <- ComBat(m_values, batch = correction_variable_1, mod = mod)
+  mod <- model.matrix(~1, data = phenodata_clean_df)
+  m_values_combat_1 <- ComBat(m_values, batch = phenodata_clean_df[,correction_variable_1], mod = mod)
   save(m_values_combat_1, 
        file = paste0(user_choices$project_name, "/processed_data/m_values_unfiltered_combat_1_", correction_variable_1,".Rdata"))
   print(paste0("M-values were first corrected for ", correction_variable_1," and were saved to the processed_data folder"))
@@ -224,8 +231,8 @@ if (correction_variable_1 == "PLEASE FILL IN"){
 if (correction_variable_2 == "PLEASE FILL IN"){
   print("No second batch correction variable was specified by user, data remains unchanged")
 } else {
-  mod <- model.matrix(~1, data = PhenoData_clean)
-  m_values_combat_2 <- ComBat(m_values_combat_1, batch = correction_variable_2, mod = mod)
+  mod <- model.matrix(~1, data = phenodata_clean_df)
+  m_values_combat_2 <- ComBat(m_values_combat_1, batch = phenodata_clean_df[,correction_variable_2], mod = mod)
   save(m_values_combat_2, file = paste0(user_choices$project_name, 
                                         "/processed_data/m_values_unfiltered_combat_2_", correction_variable_2,".Rdata"))
   print(paste0("Second, M-values were corrected for ", correction_variable_2," and were saved to the processed data folder"))
@@ -383,8 +390,8 @@ if (correction_variable_2 == "PLEASE FILL IN"){
 if (correction_variable_3 == "PLEASE FILL IN"){
   print("No third batch correction variable was specified by user, data remains unchanged")
 } else {
-  mod <- model.matrix(~1, data = PhenoData_clean)
-  m_values_combat_3 <- ComBat(m_values_combat_2, batch = correction_variable_3, mod = mod)
+  mod <- model.matrix(~1, data = phenodata_clean_df)
+  m_values_combat_3 <- ComBat(m_values_combat_2, batch = phenodata_clean_df[,correction_variable_3], mod = mod)
   save(m_values_combat_3, 
        file = paste0(user_choices$project_name, "/processed_data/m_values_unfiltered_combat_3_", correction_variable_3,".Rdata"))
   print(paste0("Third, M-values were corrected for ", correction_variable_3," and were saved to the processed_data folder"))

diff --git a/scripts/9_correction_batch_effects_filtered.Rmd b/scripts/9_correction_batch_effects_filtered.Rmd
@@ -64,6 +64,13 @@ knitr::opts_chunk$set(echo = FALSE)
 summary_table_preprocessing <- readRDS(paste0(user_choices$project_name, "/reports/summary_table_preprocessing.rds"))
 load(paste0(user_choices$project_name, "/processed_data/Betas_clean_filtered_quantile_bmiq.Rdata"))
 load(paste0(user_choices$project_name, "/processed_data/PhenoData_clean.Rdata"))
+phenodata_clean_df <- as.data.frame(PhenoData_clean@listData) %>%
+    dplyr::select(personid, plate, slide, array, row, column, arrayid) %>%
+  mutate(plate = as.factor(plate),
+         slide = as.factor(slide),
+         array = as.factor(array),
+         row = as.factor(row),
+         column = as.factor(column))
 phenotype_data <- readRDS(paste0(user_choices$project_name, "/processed_data/phenotype_data.rds"))
 ```
 
@@ -75,8 +82,8 @@ m_values <- apply(Betas_clean_filtered_quantile_bmiq, 2, function(x) log2((x)/(1
 if (correction_variable_1 == "PLEASE FILL IN"){
   print("No first batch correction variable was specified by user, data remains unchanged")
 } else {
-  mod <- model.matrix(~1, data = PhenoData_clean)
-  m_values_combat_1 <- ComBat(m_values, batch = correction_variable_1, mod = mod)
+  mod <- model.matrix(~1, data = phenodata_clean_df)
+  m_values_combat_1 <- ComBat(m_values, batch = phenodata_clean_df[,correction_variable_1], mod = mod)
   save(m_values_combat_1, 
        file = paste0(user_choices$project_name, "/processed_data/m_values_filtered_combat_1_", correction_variable_1,".Rdata"))
   print(paste0("M-values were first corrected for ", correction_variable_1," and were saved to the processed_data folder"))
@@ -234,8 +241,8 @@ if (correction_variable_1 == "PLEASE FILL IN"){
 if (correction_variable_2 == "PLEASE FILL IN"){
   print("No second batch correction variable was specified by user, data remains unchanged")
 } else {
-  mod <- model.matrix(~1, data = PhenoData_clean)
-  m_values_combat_2 <- ComBat(m_values_combat_1, batch = correction_variable_2, mod = mod)
+  mod <- model.matrix(~1, data = phenodata_clean_df)
+  m_values_combat_2 <- ComBat(m_values_combat_1, batch = phenodata_clean_df[,correction_variable_2], mod = mod)
   save(m_values_combat_2, 
        file = paste0(user_choices$project_name, "/processed_data/m_values_filtered_combat_2_", correction_variable_2,".Rdata"))
   print(paste0("Second. M-values were corrected for ", correction_variable_2," and were saved to the processed data folder"))
@@ -393,8 +400,8 @@ if (correction_variable_2 == "PLEASE FILL IN"){
 if (correction_variable_3 == "PLEASE FILL IN"){
   print("No third batch correction variable was specified by user, data remains unchanged")
 } else {
-  mod <- model.matrix(~1, data = PhenoData_clean)
-  m_values_combat_3 <- ComBat(m_values_combat_2, batch = correction_variable_3, mod = mod)
+  mod <- model.matrix(~1, data = phenodata_clean_df)
+  m_values_combat_3 <- ComBat(m_values_combat_2, batch = phenodata_clean_df[,correction_variable_3], mod = mod)
   save(m_values_combat_3, 
        file = paste0(user_choices$project_name, "/processed_data/m_values_filtered_combat_3_", correction_variable_3,".Rdata"))
   print(paste0("Third, M-values were corrected for ", correction_variable_3," were saved to the processed_data folder"))