Update 01-limma_analysis.R

d3b-center · Sep 19, 2024 · 73f7cea · 73f7cea
1 parent 19ff2b4
commit 73f7cea
Showing 1 changed file with 8 additions and 4 deletions.
diff --git a/analyses/methylation_analysis/01-limma_analysis.R b/analyses/methylation_analysis/01-limma_analysis.R
@@ -21,11 +21,15 @@ output_dir <- opt$output_dir
 dir.create(output_dir, showWarnings = F, recursive = T)
 
 # read m-values
-methyl_m_values_full <- readRDS(opt$methyl_mat) %>%
+methyl_m_values_full <- readRDS(opt$methyl_mat) %>% 
+  dplyr::slice_head(n = 500000) %>%
   na.omit() %>%
-  dplyr::mutate('Probe_ID' = make.names(Probe_ID)) %>%
-  unique(by = 'Probe_ID') %>%
-  tibble::column_to_rownames('Probe_ID')
+  unique(by = 'Probe_ID')
+
+rownames(methyl_m_values_full) <- NULL
+
+methyl_m_values_full <- methyl_m_values_full %>%
+  tibble::column_to_rownames(var = 'Probe_ID')
 
 # read annotation
 methyl_annot_full <- data.table::fread(opt$methyl_annot) %>%