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)) }
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