Skip to content

Bug fixes #2

Merged
merged 11 commits into from
Mar 19, 2025
Prev Previous commit
Next Next commit
Fixed package names, fixed filtered probe selection, removed setting …
…sex to F for unfiltered data
Vera N. Karlbauer committed Mar 7, 2025
commit 948c335074e669eea1b08296972e7bf7d8af9383
23 changes: 9 additions & 14 deletions scripts/7_normalization.Rmd
Original file line number Diff line number Diff line change
@@ -31,7 +31,7 @@ knitr::opts_knit$set(root.dir = paste0(user_choices$personal_path, "/"))
knitr::opts_chunk$set(echo = FALSE)

if (user_choices$array_type == "v2") {
if (!("jokergoo/IlluminaHumanMethylationEPICv2manifest" %in% rownames(installed.packages()))) {
if (!("IlluminaHumanMethylationEPICv2manifest" %in% rownames(installed.packages()))) {
BiocManager::install("jokergoo/IlluminaHumanMethylationEPICv2manifest")
}
if (!("IlluminaHumanMethylationEPICv2anno.20a1.hg38" %in% rownames(installed.packages()))) {
@@ -84,27 +84,22 @@ save(gRatioSet_clean_filtered_quantile, file = paste0(user_choices$project_name,

Betas_clean_filtered_quantile <- getBeta(gRatioSet_clean_filtered_quantile)
save(Betas_clean_filtered_quantile, file = paste0(user_choices$project_name,
"/processed_data/Betas_clean_filtered_quantile.Rdata"))
Ms_clean_filtered_qunatile <- getM(gRatioSet_clean_filtered_quantile)
save(Ms_clean_filtered_qunatile, file = paste0(user_choices$project_name,
"/processed_data/Ms_clean_filtered_qunatile.Rdata"))
"/processed_data/Betas_clean_filtered_quantile.Rdata"))
Ms_clean_filtered_quantile <- getM(gRatioSet_clean_filtered_quantile)
save(Ms_clean_filtered_quantile, file = paste0(user_choices$project_name,
"/processed_data/Ms_clean_filtered_quantile.Rdata"))
# further normalization with BMIQ:
probeType <- as.data.frame(annotations_clean_filtered[rownames(Betas_clean_filtered_quantile),c("Name","Type")])
probeType <- as.data.frame(subset(annotations_clean_filtered, Name %in% rownames(Betas_clean_filtered_quantile), select=c("Name","Type")))
probeType$probeType = ifelse(probeType$Type %in% "I", 1, 2)
Betas_clean_filtered_quantile_bmiq <- apply(Betas_clean_filtered_quantile[,1:length(colnames(Betas_clean_filtered_quantile))],2,
function(a) BMIQ(a,probeType$probeType,plots=FALSE)$nbeta) # sourced from script "BMIQ_1.6_Teschendorff.R"
save(Betas_clean_filtered_quantile_bmiq, file = paste0(user_choices$project_name,
"/processed_data/Betas_clean_filtered_quantile_bmiq.Rdata"))
save(Betas_clean_filtered_quantile_bmiq, file = paste0(user_choices$project_name, "/processed_data/Betas_clean_filtered_quantile_bmiq.Rdata"))

```

```{r. normalize unfiltered probes, include=FALSE}
```{r normalize unfiltered probes, include=FALSE}
# Normalization of unfiltered data

# Functional normalization
# Note: sex is set to "F" for all samples since sex chromosomes were already removed in script 6
# Note: This does not affect the normalization or the phenotype data, it simply stops preprocessQuantile() from producing an error
gRatioSet_clean_unfiltered_quantile <- preprocessQuantile(RGSet_clean, sex = "F")
gRatioSet_clean_unfiltered_quantile <- preprocessQuantile(RGSet_clean)
save(gRatioSet_clean_unfiltered_quantile, file = paste0(user_choices$project_name,
"/processed_data/gRatioSet_clean_unfiltered_quantile.Rdata")) # output: GenomicRatioSet