Nothing
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"))
}
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