tests/testthat/test_filtering.R

In OUTRIDER: OUTRIDER - OUTlier in RNA-Seq fInDER

context("Testing filtering: ")

test_that("Expression filtering", {
    library(TxDb.Hsapiens.UCSC.hg19.knownGene)
    library(org.Hs.eg.db)
    txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
    #map <- select(org.Hs.eg.db, keys=keys(txdb, keytype = "GENEID"), 
    #              keytype="ENTREZID", columns=c("SYMBOL"))
    
    ods <- makeExampleOutriderDataSet(dataset='KremerNBader')
    
    expect_error(filterExpression(ods), 
            'rowRanges\\(object\\) has all ranges of.* FPKM values')
    
    expect_warning(filterExpression(ods, gtfFile=txdb), 
            'Some genes \\(n=(770|999|783)\\) are not found')
    
    #expect_warning(filterExpression(ods, gtfFile=txdb, mapping=map, save=TRUE), 
    #        'Some genes \\(n=(17[72]|93|91)\\) are not found')
    
    ods <- filterExpression(ods, gtfFile=txdb, addExpressedGenes=TRUE)
    
    expect_true(all(
        c('expressedGenes', 'unionExpressedGenes', 'intersectionExpressedGenes',
          'passedFilterGenes', 'expressedGenesRank', 'sampleID') 
        %in% colnames(colData(ods))
        )
    )
    # Test plotting
    expect_is(plotExpressedGenes(ods), 'ggplot')    
    
})