From b25f14196dd0dcd525a1d2ec6ee1385edc2ff0d7 Mon Sep 17 00:00:00 2001 From: Natan Yusupov Date: Thu, 28 Mar 2024 13:54:25 +0100 Subject: [PATCH] annotation filtered added and code adapted --- scripts/6_filtering_cpgs.Rmd | 6 +++++- scripts/7_normalization.Rmd | 2 +- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/scripts/6_filtering_cpgs.Rmd b/scripts/6_filtering_cpgs.Rmd index 4182fb8..dfe4e50 100644 --- 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 index 717691a..99ad304 100644 --- 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")) ```