Fixed error when saving gRatioSet, moved annotation of filtered probe…

…s from script 7 to script 6.
mpip · Aug 13, 2024 · 2a8d81d · 2a8d81d
1 parent 6636b22
commit 2a8d81d
Showing 1 changed file with 5 additions and 2 deletions.
diff --git a/scripts/6_filtering_cpgs.Rmd b/scripts/6_filtering_cpgs.Rmd
@@ -418,7 +418,7 @@ if (user_choices$array_type == "v2") {
 ```
 
 ```{r, save data, include=FALSE}
-save(dim_gRatioSet_filtered, file = paste0(user_choices$project_name, "/processed_data/gRatioSet_clean_filtered.Rdata"))
+save(gRatioSet_filtered, file = paste0(user_choices$project_name, "/processed_data/gRatioSet_clean_filtered.Rdata"))
 
 Betas_clean_filtered <- getBeta(gRatioSet_clean_filtered) # beta values
 save(Betas_clean_filtered, file = paste0(user_choices$project_name, "/processed_data/Betas_clean_filtered.Rdata"))
@@ -428,8 +428,11 @@ save(Ms_clean_filtered, file = paste0(user_choices$project_name, "/processed_dat
 ```
 
 ```{r, save annotations, include=FALSE}
+# unfiltered
 save(annotations_clean, file = paste0(user_choices$project_name, "/reports/annotations_clean.Rdata"))
-
+# filtered
+annotations_clean_filtered <- getAnnotation(gRatioSet_clean_filtered)
+save(annotations_clean_filtered, file = paste0(user_choices$project_name, "/reports/annotations_clean_filtered.Rdata"))
 ```
 
 ## Beta values distribution report