Fixed names of beta objects, added dplyr specification to filter func…

…tions

scripts/11_annotate_hg19_create_pseudo_epicv1_from_epicv2.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "Script 11: Create hg19 annotation for EPICv2 and pseudo-EPICv1 version from EPICv2 data"
-date: '`r format(Sys.time(), %d %B, %Y")`'
+date: '`r format(Sys.time(), "%d %B, %Y")`'
 output: html_document
 ---
 
@@ -27,11 +27,10 @@ start_time <- Sys.time()
 
 ```{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$package_directory != "PLEASE FILL IN"){
-  .libPaths(c(user_choices$package_directory, .libPaths()))
+if(user_choices$package_path != "PLEASE FILL IN"){
+  .libPaths(c(user_choices$package_path, .libPaths()))
 }
 
 needed_packages <- c("BiocManager", "dplyr", "knitr", "rmarkdown", "tibble", "minfi", "janitor")
@@ -57,6 +56,7 @@ load(paste0(user_choices$project_name, "/reports/annotations_clean_unfiltered.Rd
 load(paste0(user_choices$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}
@@ -68,7 +68,7 @@ if (user_choices$array_type == "v1") {
 
 ```{r, hg19 annotation filtered data, include = FALSE}
 annations_clean_filtered_hg19 <- annotation_hg19 %>%
-  dplyr::filter(Probe_ID %in% rownames(Betas_clean_quantile_bmiq_filtered_combated))
+  dplyr::filter(Probe_ID %in% rownames(Betas_clean_filtered_quantile_bmiq_combated))
 save(annations_clean_filtered_hg19, file = paste0(user_choices$project_name, "/reports/annations_clean_filtered_hg19.Rdata"))
 ```
 
@@ -81,10 +81,10 @@ 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 %>%
-  filter(Name %in% rownames(Betas_clean_filtered_quantile_bmiq_combated)) %>%
+  dplyr::filter(Name %in% rownames(Betas_clean_filtered_quantile_bmiq_combated)) %>%
   # only keep loci on EPICv1, filter wrongly annotated empty value
-  filter(EPICv1_Loci != "") %>%
-  filter(duplicated(EPICv1_Loci) == FALSE)
+  dplyr::filter(EPICv1_Loci != "") %>%
+  dplyr::filter(duplicated(EPICv1_Loci) == FALSE)
 
 # only keep betas that are on v1 and exclude any duplicated loci (keep first CpG)
 keep_betas <- (rownames(Betas_clean_filtered_quantile_bmiq_combated) %in% annotations_clean_filtered_pseudo_v1$Name)
@@ -103,7 +103,7 @@ save(Betas_clean_filtered_quantile_bmiq_combated_pseudo_v1, file = paste0(user_c
   cat(paste0(keep_betas_df %>% filter(keep_betas == FALSE) %>% nrow(), 
              " filtered CpGs were not found on EPICv1 and therefore excluded"), sep = "<br>\n")
 
-  dim_Betas_filtered <- dim(Betas_clean_quantile_bmiq_filtered_combated_pseudo_v1)
+  dim_Betas_filtered <- dim(Betas_clean_filtered_quantile_bmiq_combated_pseudo_v1)
   step_number <- c("14")
   step <- c("Create pseudo-EPICv1 version (filtered data)")
   data_class <- c("Betas")
@@ -117,9 +117,9 @@ 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 %>%
-  filter(Name %in% rownames(Betas_clean_unfiltered_quantile_bmiq_combated)) %>%
-  filter(EPICv1_Loci != "") %>%
-  filter(duplicated(EPICv1_Loci) == FALSE)
+  dplyr::filter(Name %in% rownames(Betas_clean_unfiltered_quantile_bmiq_combated)) %>%
+  dplyr::filter(EPICv1_Loci != "") %>%
+  dplyr::filter(duplicated(EPICv1_Loci) == FALSE)
 
 # only keep betas that are on v1 and exclude any duplicated loci (keep first CpG)
 keep_betas <- (rownames(Betas_clean_unfiltered_quantile_bmiq_combated) %in% annotations_clean_unfiltered_pseudo_v1$Name)
@@ -138,7 +138,7 @@ save(Betas_clean_unfiltered_quantile_bmiq_combated_pseudo_v1, file = paste0(user
   cat(paste0(keep_betas_df %>% filter(keep_betas == FALSE) %>% nrow(), 
              " unfiltered CpGs were not found on EPICv1 and therefore excluded"), sep = "<br>\n")
 
-  dim_Betas_unfiltered <- dim(Betas_clean_quantile_bmiq_unfiltered_combated_pseudo_v1)
+  dim_Betas_unfiltered <- dim(Betas_clean_unfiltered_quantile_bmiq_combated_pseudo_v1)
   step_number <- c("15")
   step <- c("Create pseudo-EPICv1 version (unfiltered data)")
   data_class <- c("Betas")