Fixed typos, correct name of source scripts, print PCA tables in extr…

…a chunks

scripts/10_correction_batch_effects_unfiltered.Rmd

@@ -30,7 +30,7 @@ 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")
@@ -69,7 +69,7 @@ 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_unfiltered_quantile_bmiq, 2, function(x) log2((x)/(1-x))) # get M-values
 
 if (correction_variable_1 == "PLEASE FILL IN"){
@@ -230,7 +230,11 @@ 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 {
@@ -389,7 +393,11 @@ if (correction_variable_2 == "PLEASE FILL IN"){
 }
 ```
 
-```{r, correction of third batch effect and PCA}
+```{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, results='asis'}
 if (correction_variable_3 == "PLEASE FILL IN"){
   print("No third batch correction variable was specified by user, data remains unchanged")
 } else {
@@ -548,7 +556,11 @@ if (correction_variable_3 == "PLEASE FILL IN"){
 }
 ```
 
-```{r, convertion M to Beta and save, include=FALSE}
+```{r, print p-value table for batch effects after correction of third batch effect variable}
+anova_lm_pvalue_df %>% paged_table()
+```
+
+```{r, conversion M to Beta and save, include=FALSE}
 if(exists("m_values_combat_3")){
   corrected_data <- m_values_combat_3
   changing_status <- "changed"