diff --git a/analyses/dge_pathway_analysis/01-dge_analysis_deseq.R b/analyses/dge_pathway_analysis/01-dge_analysis_deseq.R index 0f3a675..fd2cd04 100644 --- a/analyses/dge_pathway_analysis/01-dge_analysis_deseq.R +++ b/analyses/dge_pathway_analysis/01-dge_analysis_deseq.R @@ -92,7 +92,7 @@ for (i in 1:length(clusters)) { output_df <- rbind(output_df, deseq_output) # pathway enrichment using REACTOME - cat('Running Reactome pathway enrichment') + cat('Running Reactome pathway enrichment \n') reactome_pathways <- msigdbr::msigdbr(category = "C2", subcategory = "CP:REACTOME") reactome_pathways <- reactome_pathways %>% dplyr::select(gs_name, gene_symbol) %>% @@ -108,7 +108,7 @@ for (i in 1:length(clusters)) { ) # pathway enrichment using HALLMARK - cat('Running Hallmark pathway enrichment') + cat('Running Hallmark pathway enrichment \n') hallmark_pathways <- msigdbr::msigdbr(category = "H", subcategory = NULL) hallmark_pathways <- hallmark_pathways %>% dplyr::select(gs_name, gene_symbol) %>% @@ -125,6 +125,6 @@ for (i in 1:length(clusters)) { } # write output to tsv -cat('Writing outputs') +cat('Writing outputs \n') write_tsv(x = output_df, file = file.path(results_dir, "diffexpr_output_per_cluster.tsv"))