From abfde6e34dca6c1cbba7dc1a079a22721bc0be12 Mon Sep 17 00:00:00 2001 From: aadamk Date: Wed, 9 Oct 2024 10:34:17 -0400 Subject: [PATCH] Update 01-limma_analysis.R --- analyses/methylation_analysis/01-limma_analysis.R | 2 ++ 1 file changed, 2 insertions(+) diff --git a/analyses/methylation_analysis/01-limma_analysis.R b/analyses/methylation_analysis/01-limma_analysis.R index a513ac9..049ad5a 100644 --- a/analyses/methylation_analysis/01-limma_analysis.R +++ b/analyses/methylation_analysis/01-limma_analysis.R @@ -23,6 +23,7 @@ output_dir <- opt$output_dir dir.create(output_dir, showWarnings = F, recursive = T) # read m-values +cat('Reading m-values') methyl_m_values_full <- readRDS(opt$methyl_mat) %>% dplyr::slice_head(n = 500000) %>% na.omit() %>% @@ -31,6 +32,7 @@ methyl_m_values_full <- methyl_m_values_full %>% tibble::column_to_rownames('Probe_ID') # read annotation +cat('Reading methylation feature annotations') methyl_annot_full <- data.table::fread(opt$methyl_annot) %>% dplyr::filter(!duplicated(Probe_ID))