In RGLab/ImmuneSignatures2: Pre-Processing for HIPC ImmuneSignatures2 Analysis

knitr::opts_chunk$set(echo = FALSE, include = FALSE)

library(ImmuneSignatures2) # vaccine map loaded as `vaccines`
library(Biobase)
library(here)

dataCacheDir <- here("data_cache", "old")
inputFilenamePrefix <- "2020_10_27_"

files <- list.files(dataCacheDir, pattern = paste0(inputFilenamePrefix, ".+set.rds"))
for (filename in files) {
  eset <- readRDS(file.path(dataCacheDir, filename))
  pd <- pData(eset)
  y_chrom_present <- ifelse(pd$gender_imputed == "Male", TRUE, FALSE)
  y_chrom_present_timepoint <- ifelse(pd$gender_imputed_timepoint == "Male", TRUE, FALSE)
  failedYchromQC <- pd$failedGenderQC
  pd <- cbind(pd, y_chrom_present, y_chrom_present_timepoint, failedYchromQC)
  pData(eset) <- pd
  saveRDS(eset, file.path(dataCacheDir, "ychrom", filename))
}