annotation filtered added and code adapted

mpip · Mar 28, 2024 · b25f141 · b25f141
1 parent 612127d
commit b25f141
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diff --git a/scripts/6_filtering_cpgs.Rmd b/scripts/6_filtering_cpgs.Rmd
@@ -32,7 +32,6 @@ load(paste0(user_choices$project_name, "/processed_data/RGSet_clean.Rdata"))
 load(paste0(user_choices$project_name, "/processed_data/Betas_clean.Rdata"))
 load(paste0(user_choices$project_name, "/processed_data/PhenoData_clean.Rdata"))
 load(paste0(user_choices$project_name, "/processed_data/detP_clean.Rdata"))
-load(paste0(user_choices$project_name, "/reports/annotations_clean.Rdata"))
 # Info about cross-hybridizing probes comes from Chen et al. 2013, DOI: 10.4161/epi.23470:
 load("data/ChenProbeIDs.rdata")
 ```
@@ -50,6 +49,11 @@ We will remove probes that:
 * cross-hybridize (described by McCartney et al.)  
 * are polymorphic  
 
+```{r get annotation of probes, include=FALSE}
+annotations_clean = getAnnotation(RGSet_clean)
+save(annotations_clean, file = paste0(user_choices$project_name, "/reports/annotations_clean.Rdata"))
+```
+
 ## Removal of failed probes in one or more samples
 
 ```{r filter out failed probes, include=FALSE}

diff --git a/scripts/7_normalization.Rmd b/scripts/7_normalization.Rmd
@@ -64,7 +64,7 @@ data for further investigation. These files are saved to reports folder.
 **Note**  
 The user can further alter the normalization methods if needed (e.g. include noob etc.)  
 
-```{r get annotation of probes, include=FALSE}
+```{r get annotation of filtered probes, include=FALSE}
 annotations_clean_filtered = getAnnotation(RGSet_clean_filtered)
 save(annotations_clean_filtered, file = paste0(user_choices$project_name, "/reports/annotations_clean_filtered.Rdata"))
 ```