tests/testthat/test-getters.R

In ChIPSeqSpike: ChIP-Seq data scaling according to spike-in control

## Preparing data
file_vec <- system.file("extdata", 
        c("bam_files/H3K79me2_0_dm3-filtered.bam", 
                "bam_files/H3K79me2_0_hg19-filtered.bam", 
                "bigwig_files/H3K79me2_0-filtered.bw", 
                "bigwig_files/input_0-filtered.bw", 
                "bam_files/input_0_hg19-filtered.bam"),
        package="ChIPSeqSpike")

e <- Experiment(endogenousBamFilePath = file_vec[2], 
        exogenousBamFilePath = file_vec[1], 
        bigWigFilePath = file_vec[3], 
        name = "H3K79me2_0", endoScalingFactor = 1, exoScalingFactor = 2, 
        endoNb = 3, exoNb = 4)

eboost <- ExperimentLoaded(endogenousBamFilePath = file_vec[2], 
        exogenousBamFilePath = file_vec[1], 
        bigWigFilePath = file_vec[3], 
        name = "H3K79me2_0", endoScalingFactor = 1, exoScalingFactor = 2, 
        endoNb = 3, exoNb = 4)

csds <- ChIPSeqSpikeDataset(endogenousBam_vec = file_vec[2],
        exogenousBam_vec = file_vec[1],
        bigWigFile_endogenous_vec = file_vec[3], 
        inputBigWigFile = file_vec[4], 
        inputBamFile = file_vec[5], 
        expnames = "H3K79me2_0", inputSF = 0.7, inputNb = 1000)

csdsboost <- ChIPSeqSpikeDatasetBoost(endogenousBam_vec = file_vec[2],
        exogenousBam_vec = file_vec[1],
        bigWigFile_endogenous_vec = file_vec[3], 
        inputBigWigFile = file_vec[4], 
        inputBamFile = file_vec[5], 
        expnames = "H3K79me2_0", inputSF = 0.7, inputNb = 1000)

spikesumtest <- matrix(c(0,0.7,0,NA,0,1000,0,NA), ncol=4, nrow=2)
colnames(spikesumtest) <- c("endoScalFact", "exoScalFact", "endoCount", 
        "exoCount")
rownames(spikesumtest) <- c("H3K79me2_0", "input")

ratiotest <- matrix(0)
colnames(ratiotest) <- "Percentage Exo"
rownames(ratiotest) <- "H3K79me2_0"

## Testing accessors to all types of object

context("Testing proper accession to objects")

test_that("Accessors of Experiment object are valid", {
            
            expect_equal(getBam(e), file_vec[2])
            expect_equal(getExogenousBam(e), file_vec[1])
            expect_equal(getBigWigFile(e), file_vec[3])
            expect_equal(getExpName(e), "H3K79me2_0")
            expect_equal(getScalingFactor(e), 1)
            expect_equal(getExogenousScalingFactor(e), 2)
            expect_equal(getCount(e), 3)
            expect_equal(getExoCount(e), 4)
        })

if(.Platform$OS.type != 'windows') {
    
    test_that("Accessors of ExperimentLoaded object are valid", {
                
                expect_equal(getBam(eboost), file_vec[2])
                expect_equal(getExogenousBam(eboost), file_vec[1])
                expect_equal(getBigWigFile(eboost), file_vec[3])
                expect_equal(getExpName(eboost), "H3K79me2_0")
                expect_equal(getScalingFactor(eboost), 1)
                expect_equal(getExogenousScalingFactor(eboost), 2)
                expect_equal(getCount(eboost), 3)
                expect_equal(getExoCount(eboost), 4)
            })
}

test_that("Accessors to ChIPSeqSpikeDataset are valid", {
            
            expect_equal(getBam(csds), file_vec[5])
            expect_equal(getBigWigFile(csds), file_vec[4])
            expect_equal(as.character(getExperimentListBigWigs(csds)), 
                    file_vec[3])
            expect_equal(getExpName(csds), "H3K79me2_0")
            expect_equal(getScalingFactor(csds), 0.7)
            expect_equal(getCount(csds), 1000)
            expect_equal(spikeSummary(csds), spikesumtest)
            suppressWarnings(expect_equal(getRatio(csds), ratiotest))
        })

if(.Platform$OS.type != 'windows') {
    test_that("Accessors to ChIPSeqSpikeDatasetBoost are valid", {
                
                expect_equal(getBam(csdsboost), file_vec[5])
                expect_equal(getBigWigFile(csdsboost), file_vec[4])
                expect_equal(as.character(getExperimentListBigWigs(csdsboost)), 
                        file_vec[3])
                expect_equal(getExpName(csdsboost), "H3K79me2_0")
                expect_equal(getScalingFactor(csdsboost), 0.7)
                expect_equal(getCount(csdsboost), 1000)
                expect_equal(spikeSummary(csdsboost), spikesumtest)
                suppressWarnings(expect_equal(getRatio(csds), ratiotest))
            })
}