diff --git a/program/shinyApp/R/enrichment_analysis/enrichment_analysis.R b/program/shinyApp/R/enrichment_analysis/enrichment_analysis.R index 32a7a091..276319da 100644 --- a/program/shinyApp/R/enrichment_analysis/enrichment_analysis.R +++ b/program/shinyApp/R/enrichment_analysis/enrichment_analysis.R @@ -76,14 +76,14 @@ gene_set_enrichment <- function( ){ EnrichmentRes_GO <- clusterProfiler::gseGO( gene = geneSetChoice, - ont = input$ontologyForGO, + ont = "All", keyType = "ENTREZID", minGSSize = 3, maxGSSize = 800, pvalueCutoff = 0.05, verbose = TRUE, OrgDb = ifelse(input$OrganismChoice == "hsa","org.Hs.eg.db","org.Mm.eg.db"), - pAdjustMethod = "none" # TODO: discuss + pAdjustMethod = PADJUST_METHOD[[adjustMethod]] ) res_tmp$EA[[comp_type]][[contrast]]$GO <<- EnrichmentRes_GO par_tmp$EA[[comp_type]][[contrast]]$GO <<- list("adjustMethod"=adjustMethod, "sort"=sorting)