Correct name of source script and print batch effect tables in separa…

…te chunks

scripts/9_correction_batch_effects_filtered.Rmd

@@ -41,7 +41,7 @@ start_time <- Sys.time()
 ```
 
 ```{r setup, include=FALSE}
-source("../data/calculate_pc_cutoff.R") # source function for determining PC cutoff 
+source("../data/Calculate_PC_Cutoff.R") # source function for determining PC cutoff 
 needed_packages <- c("BiocManager", "dplyr", "knitr", "rmarkdown", "tibble", "ggplot2", 
                      "ggrepel", "broom", "gplots", "tidyr", "sva", "methods")
 user_choices <- readRDS("../data/user_choices.rds")
@@ -79,7 +79,7 @@ phenotype_data <- readRDS(paste0(user_choices$project_name, "/processed_data/phe
 
 ## Correction of technical batch effects with ComBat
 
-```{r, correction of first batch effect and PCA}
+```{r, correction of first batch effect and PCA, results='asis'}
 m_values <- apply(Betas_clean_filtered_quantile_bmiq, 2, function(x) log2((x)/(1-x))) # get M-values
 
 if (correction_variable_1 == "PLEASE FILL IN"){
@@ -240,7 +240,11 @@ if (correction_variable_1 == "PLEASE FILL IN"){
 }
 ```
 
-```{r, correction of second batch effect and PCA}
+```{r, print p-value table for batch effects after correction of first batch effect variable}
+anova_lm_pvalue_df %>% paged_table()
+```
+
+```{r, correction of second batch effect and PCA, results='asis'}
 if (correction_variable_2 == "PLEASE FILL IN"){
   print("No second batch correction variable was specified by user, data remains unchanged")
 } else {
@@ -399,6 +403,10 @@ if (correction_variable_2 == "PLEASE FILL IN"){
 }
 ```
 
+```{r, print p-value table for batch effects after correction of second batch effect variable}
+anova_lm_pvalue_df %>% paged_table()
+```
+
 ```{r, correction of third batch effect and PCA}
 if (correction_variable_3 == "PLEASE FILL IN"){
   print("No third batch correction variable was specified by user, data remains unchanged")
@@ -557,6 +565,10 @@ if (correction_variable_3 == "PLEASE FILL IN"){
 }
 ```
 
+```{r, print p-value table for batch effects after correction of third batch effect variable}
+anova_lm_pvalue_df %>% paged_table()
+```
+
 ```{r, convertion M to Beta and save, include=FALSE}
 if(exists("m_values_combat_3")){
   corrected_data <- m_values_combat_3