Fix probe exclusion in filtered data, add individual beta density plo…

…ts after BMIQ

scripts/7_normalization.Rmd

@@ -71,10 +71,8 @@ The user can further alter the normalization methods if needed (e.g. include noo
 ```{r normalize filtered probes, include=FALSE}
 # Normalization of filtered data
 
-# Matrix of probes removed in all prior filtering steps
-exclusion_matrix <- Betas_clean[!rownames(Betas_clean) %in% rownames(Betas_clean_filtered), ]
 # Exclude all probes filtered script 5 from steps before to improve preprocessing
-RGSet_clean_filtered <- subsetByLoci(RGSet_clean, excludeLoci = rownames(exclusion_matrix))
+RGSet_clean_filtered <- subsetByLoci(RGSet_clean, includeLoci = rownames(Betas_clean_filtered))
 # Functional normalization 
 # Note: sex is set to "F" for all samples since sex chromosomes were already removed in script 6
 # Note: This does not affect the normalization or the phenotype data, it simply stops preprocessQuantile() from producing an error
@@ -180,6 +178,24 @@ for (i in 1:ncol(Betas_clean_unfiltered_quantile)) {
   densityPlot(i_mat, pal = "darkblue", main = names_unfiltered_quantileBetas[i])
 }
 dev.off()
+
+names_filtered_quantileBetas_bmiq <- colnames(Betas_clean_filtered_quantile_bmiq)
+pdf(paste0(user_choices$project_name, "/reports/beta_densities_filtered_quantile_normalized_bmiq.pdf"))
+for (i in 1:ncol(Betas_clean_filtered_quantile_bmiq)) {
+  i_mat <- as.matrix(Betas_clean_filtered_quantile_bmiq[ ,i])
+  name <- colnames(Betas_clean_filtered_quantile_bmiq[,i])
+  densityPlot(i_mat, pal = "darkblue", main = names_filtered_quantileBetas_bmiq[i])
+}
+dev.off()
+
+names_unfiltered_quantileBetas_bmiq <- colnames(Betas_clean_unfiltered_quantile_bmiq)
+pdf(paste0(user_choices$project_name, "/reports/beta_densities_unfiltered_quantile_normalized_bmiq.pdf"))
+for (i in 1:ncol(Betas_clean_unfiltered_quantile_bmiq)) {
+  i_mat <- as.matrix(Betas_clean_unfiltered_quantile_bmiq[ ,i])
+  name <- colnames(Betas_clean_unfiltered_quantile_bmiq[,i])
+  densityPlot(i_mat, pal = "darkblue", main = names_unfiltered_quantileBetas_bmiq[i])
+}
+dev.off()
 ```
 
 ## User report