tests/testthat/test-compareCluster.R

In YuLab-SMU/clusterProfiler: A universal enrichment tool for interpreting omics data

# data(geneList, package="DOSE")

# mydf <- data.frame(Entrez=names(geneList), FC=geneList)
# mydf <- mydf[abs(mydf$FC) > 1,]
# mydf$group <- "upregulated"
# mydf$group[mydf$FC < 0] <- "downregulated"
# mydf$othergroup <- "A"
# mydf$othergroup[abs(mydf$FC) > 2] <- "B"

# test_that("enrichGO formula interface works", {
#   formula_res <- compareCluster(
#     Entrez ~ group + othergroup,
#     data = mydf, fun = "enrichGO", OrgDb = org.Hs.eg.db)

#   expect_true(is(formula_res, "compareClusterResult"))
#   expect_equal(formula_res@fun, "enrichGO")
#   expect_true(all(sapply(formula_res@geneClusters, function(x) is.character(x))))
# })

# test_that("gseGO formula interface works", {
#   formula_res <- compareCluster(
#     Entrez | FC ~ group + othergroup,
#     data = mydf, fun = "gseGO", OrgDb = org.Hs.eg.db)

#   expect_true(is(formula_res, "compareClusterResult"))
#   expect_equal(formula_res@fun, "gseGO")
#   expect_true(all(sapply(formula_res@geneClusters, function(x) is.numeric(x))))
# })