From f5c5dbf80bf83f59acf5dd041d046fe49a97b331 Mon Sep 17 00:00:00 2001 From: aadamk Date: Wed, 9 Oct 2024 10:26:41 -0400 Subject: [PATCH] Update 01-dge_analysis_deseq.R --- analyses/dge_pathway_analysis/01-dge_analysis_deseq.R | 3 +++ 1 file changed, 3 insertions(+) diff --git a/analyses/dge_pathway_analysis/01-dge_analysis_deseq.R b/analyses/dge_pathway_analysis/01-dge_analysis_deseq.R index 285ff89..0f3a675 100644 --- a/analyses/dge_pathway_analysis/01-dge_analysis_deseq.R +++ b/analyses/dge_pathway_analysis/01-dge_analysis_deseq.R @@ -92,6 +92,7 @@ for (i in 1:length(clusters)) { output_df <- rbind(output_df, deseq_output) # pathway enrichment using REACTOME + cat('Running Reactome pathway enrichment') reactome_pathways <- msigdbr::msigdbr(category = "C2", subcategory = "CP:REACTOME") reactome_pathways <- reactome_pathways %>% dplyr::select(gs_name, gene_symbol) %>% @@ -107,6 +108,7 @@ for (i in 1:length(clusters)) { ) # pathway enrichment using HALLMARK + cat('Running Hallmark pathway enrichment') hallmark_pathways <- msigdbr::msigdbr(category = "H", subcategory = NULL) hallmark_pathways <- hallmark_pathways %>% dplyr::select(gs_name, gene_symbol) %>% @@ -123,5 +125,6 @@ for (i in 1:length(clusters)) { } # write output to tsv +cat('Writing outputs') write_tsv(x = output_df, file = file.path(results_dir, "diffexpr_output_per_cluster.tsv"))