tests/testthat/test_addGeneIDs.R

In ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

test_that("addGeneIDs works not correct", {
    data(annotatedPeak)
    x<-addGeneIDs(annotatedPeak[1:6],"org.Hs.eg.db",c("symbol","omim"))
    expect_is(x$symbol, "character")
    expect_is(x$omim, "character")
    expect_equal(x$feature[1:4], c("ENSG00000202254", "ENSG00000186086",
                              "ENSG00000065135", "ENSG00000197106"))
    expect_equal(unname(x$symbol[1:4]), c(NA, "NBPF6", "GNAI3", "SLC6A17"))
    x <- addGeneIDs(c("ENSG00000065135", "ENSG00000116396", 
                      "ENSG00000197106", "ENSG00000186086", 
                      "ENSG00000202254"), org.Hs.eg.db, c("symbol"))
    expect_equal(unname(x$symbol[match(c("ENSG00000065135", "ENSG00000116396", 
                                  "ENSG00000197106", "ENSG00000186086", 
                                  "ENSG00000202254"), x$ensembl_gene_id)]), 
                 c('GNAI3', 'KCNC4', 'SLC6A17', 'NBPF6', NA))
    expect_error(addGeneIDs("ENSG00000065135", orgAnn="generate.error"))
})