tests/testthat/test_topAnat.R

In wirawara/BgeeDB: Annotation and gene expression data retrieval from Bgee database

context("expect_output")


test_that("Creating the topAnat object is working", {
  bgee <- Bgee$new(species="Mus_musculus", dataType="rna_seq")
  myTopAnatData <- loadTopAnatData(bgee, stage="UBERON:0000068")
  geneList <- as.factor(c(rep(0, times=90), rep(1, times=10)))
  names(geneList) <- c("ENSMUSG00000064370", "ENSMUSG00000064368", "ENSMUSG00000064367",
                       "ENSMUSG00000064363", "ENSMUSG00000065947", "ENSMUSG00000064360",
                       "ENSMUSG00000064358", "ENSMUSG00000064357", "ENSMUSG00000064356",
                       "ENSMUSG00000064354", "ENSMUSG00000064351", "ENSMUSG00000064345",
                       "ENSMUSG00000064341", "ENSMUSG00000029757", "ENSMUSG00000079941",
                       "ENSMUSG00000053367", "ENSMUSG00000016626", "ENSMUSG00000037816",
                       "ENSMUSG00000036781", "ENSMUSG00000022519", "ENSMUSG00000079606",
                       "ENSMUSG00000068966", "ENSMUSG00000038608", "ENSMUSG00000047473",
                       "ENSMUSG00000038542", "ENSMUSG00000025386", "ENSMUSG00000028145",
                       "ENSMUSG00000024816", "ENSMUSG00000020978", "ENSMUSG00000055373",
                       "ENSMUSG00000038155", "ENSMUSG00000046408", "ENSMUSG00000030032",
                       "ENSMUSG00000042249", "ENSMUSG00000071909", "ENSMUSG00000039670",
                       "ENSMUSG00000032501", "ENSMUSG00000054252", "ENSMUSG00000068071",
                       "ENSMUSG00000067578", "ENSMUSG00000074892", "ENSMUSG00000027905",
                       "ENSMUSG00000058216", "ENSMUSG00000078754", "ENSMUSG00000062101",
                       "ENSMUSG00000043633", "ENSMUSG00000071350", "ENSMUSG00000021639",
                       "ENSMUSG00000059113", "ENSMUSG00000049115", "ENSMUSG00000053310",
                       "ENSMUSG00000043832", "ENSMUSG00000063767", "ENSMUSG00000026775",
                       "ENSMUSG00000038537", "ENSMUSG00000078716", "ENSMUSG00000096820",
                       "ENSMUSG00000075089", "ENSMUSG00000049971", "ENSMUSG00000014303",
                       "ENSMUSG00000056054", "ENSMUSG00000033082", "ENSMUSG00000020801",
                       "ENSMUSG00000030590", "ENSMUSG00000026188", "ENSMUSG00000014301",
                       "ENSMUSG00000073491", "ENSMUSG00000014529", "ENSMUSG00000036960",
                       "ENSMUSG00000058748", "ENSMUSG00000047388", "ENSMUSG00000002204",
                       "ENSMUSG00000034285", "ENSMUSG00000109129", "ENSMUSG00000035275",
                       "ENSMUSG00000051184", "ENSMUSG00000034424", "ENSMUSG00000041828",
                       "ENSMUSG00000029416", "ENSMUSG00000030468", "ENSMUSG00000029911",
                       "ENSMUSG00000055633", "ENSMUSG00000027495", "ENSMUSG00000029624",
                       "ENSMUSG00000045518", "ENSMUSG00000074259", "ENSMUSG00000035228",
                       "ENSMUSG00000038533", "ENSMUSG00000030401", "ENSMUSG00000014602",
                       "ENSMUSG00000041827", "ENSMUSG00000042345", "ENSMUSG00000028530",
                       "ENSMUSG00000038722", "ENSMUSG00000075088", "ENSMUSG00000039629",
                       "ENSMUSG00000067567", "ENSMUSG00000057594", "ENSMUSG00000005907",
                       "ENSMUSG00000027496")
  myTopAnatObject <-  topAnat(myTopAnatData, geneList)

  expect_is(myTopAnatObject, "topGOdata")
  expect_message( message("Annotating nodes (Can be long)......") )
})