Import annotation before changing working directorz, convert annotati…

…on to dataframe

scripts/11_annotate_hg19_create_pseudo_epicv1_from_epicv2.Rmd

@@ -25,8 +25,14 @@ This script is only intended for EPICv2 data. Do not run it on EPICv1 data.
 start_time <- Sys.time()
 ```
 
+```{r import annotation, include=FALSE}
+annotation_hg19 <- read.table("../data/EPICv2.hg19.manifest.tsv")
+annotation_hg19 <- row_to_names(annotation_hg19, row_number = 1, remove_row = TRUE, remove_rows_above = TRUE)
+```
+
 ```{r setup, include=FALSE}
 user_choices <- readRDS("../data/user_choices.rds")
+knitr::opts_knit$set(root.dir = paste0(user_choices$personal_path, "/"))
 knitr::opts_chunk$set(echo = FALSE)
 
 if(user_choices$package_path != "PLEASE FILL IN"){
@@ -54,9 +60,6 @@ load(paste0(user_choices$project_name, "/processed_data/Betas_clean_filtered_qua
 load(paste0(user_choices$project_name, "/reports/annotations_clean_filtered.Rdata"))
 load(paste0(user_choices$project_name, "/reports/annotations_clean_unfiltered.Rdata"))
 load(paste0(user_choices$project_name, "/processed_data/PhenoData_clean.Rdata"))
-annotation_hg19 <- read.table(paste0(user_choices$personal_path, "/epic_preprocessing_k2h/data/EPICv2.hg19.manifest.tsv"))
-annotation_hg19 <- row_to_names(annotation_hg19, row_number = 1, remove_row = TRUE, remove_rows_above = TRUE)
-knitr::opts_knit$set(root.dir = paste0(user_choices$personal_path, "/"))
 ```
 
 ```{r, check array type, include = TRUE}
@@ -80,7 +83,8 @@ save(annotions_clean_unfiltered_hg19, file = paste0(user_choices$project_name, "
 
 ```{r, create pseudo-EPICv1 version for filtered data, include=FALSE}
 # create annotation only containing filtered CpGs that are also on v1 and exclude any duplicated loci
-annotations_clean_filtered_pseudo_v1 <- annotations_clean_filtered %>%
+annotations_clean_filtered_pseudo_v1 <- annotations_clean_filtered@listData %>%
+  as.data.frame() %>%
   dplyr::filter(Name %in% rownames(Betas_clean_filtered_quantile_bmiq_combated)) %>%
   # only keep loci on EPICv1, filter wrongly annotated empty value
   dplyr::filter(EPICv1_Loci != "") %>%
@@ -116,7 +120,8 @@ save(Betas_clean_filtered_quantile_bmiq_combated_pseudo_v1, file = paste0(user_c
 
 ```{r, create pseudo-EPICv1 version for unfiltered data, include=FALSE}
 # create annotation only containing unfiltered CpGs that are also on v1 and exclude any duplicated loci
-annotations_clean_unfiltered_pseudo_v1 <- annotations_clean_unfiltered %>%
+annotations_clean_unfiltered_pseudo_v1 <- annotations_clean_unfiltered@listData %>%
+  as.data.frame() %>%
   dplyr::filter(Name %in% rownames(Betas_clean_unfiltered_quantile_bmiq_combated)) %>%
   dplyr::filter(EPICv1_Loci != "") %>%
   dplyr::filter(duplicated(EPICv1_Loci) == FALSE)