customEnrichment.create <- function() { enrich <- readRDS(testthat::test_path("fixtures", "clusterProfilerGSEA.RDS")) enrich <- enrich@result %>% as.data.table() %>% setnames('setSize', 'size') %>% setnames('NES', 'nes') %>% setnames('core_enrichment', 'pathwayGenes') %>% .[ , list(Description, size, nes, pathwayGenes, pvalue) ] saveRDS(enrich, testthat::test_path("fixtures", "customEnrichment.RDS")) } clusterProfilerGSEA.create <- function() { data(geneList) enrich <- clusterProfiler::gseGO(geneList, OrgDb = org.Hs.eg.db, ont = 'CC') saveRDS(enrich, testthat::test_path("fixtures", "clusterProfilerGSEA.RDS")) } clusterProfilerORA.create <- function() { data(geneList) significantUp <- names(geneList)[ geneList > 2 ] enrich <- clusterProfiler::enrichGO(significantUp, OrgDb = org.Hs.eg.db, ont = 'CC', universe = names(geneList)) saveRDS(enrich, testthat::test_path("fixtures", "clusterProfilerORA.RDS")) } gprofiler.create() <- function() { data(geneList) query <- geneList[ c(1:1000, (length(geneList) - 1000):(length(geneList))) ] %>% names() enrich <- gprofiler2::gost(query, organism = 'hsapiens', evcodes = TRUE) saveRDS(enrich, testthat::test_path("fixtures", "gprofiler2.RDS")) }