Update 02-dms_gsameth_analysis.R

d3b-center · Oct 9, 2024 · 4c85737 · 4c85737
1 parent abfde6e
commit 4c85737
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/analyses/methylation_analysis/02-dms_gsameth_analysis.R b/analyses/methylation_analysis/02-dms_gsameth_analysis.R
@@ -31,6 +31,7 @@ plots_dir <- opt$plots_dir
 dir.create(plots_dir, showWarnings = F, recursive = T)
 
 # genesets
+cat('Reading pathway annotations')
 if (msigdb == "kegg") {
   category <- "C2"
   subcategory = "CP:KEGG"
@@ -51,6 +52,7 @@ gene_set_entrez <- base::split(gene_set$entrez_gene, list(gene_set$gs_name))
 diffexpr_sites <- read_tsv(diffexpr_sites)
 
 # read methylation matrix for pulling all probes used in the analysis
+cat('Reading methylation values')
 methyl_mat <- readRDS(methyl_mat) %>% 
   dplyr::slice_head(n = 500000) %>%
   na.omit() %>%