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Fixed names of beta objects, added dplyr specification to filter func…
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…tions
Vera N. Karlbauer committed Mar 7, 2025
1 parent e03628b commit f1bd3ab
Showing 1 changed file with 13 additions and 13 deletions.
26 changes: 13 additions & 13 deletions scripts/11_annotate_hg19_create_pseudo_epicv1_from_epicv2.Rmd
Original file line number Diff line number Diff line change
@@ -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")

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