From 2a8d81db3f6cfa9211b039ea800d5e91b475b84f Mon Sep 17 00:00:00 2001 From: "Vera N. Karlbauer" Date: Tue, 13 Aug 2024 16:53:46 +0200 Subject: [PATCH] Fixed error when saving gRatioSet, moved annotation of filtered probes from script 7 to script 6. --- scripts/6_filtering_cpgs.Rmd | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/scripts/6_filtering_cpgs.Rmd b/scripts/6_filtering_cpgs.Rmd index 55bdf32..2cd42c2 100644 --- 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