tests/testthat/test-functions.R

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

## Preparing data for testing


indir <- system.file("extdata", package="airway", mustWork=TRUE)

file_vec <- system.file(
        c("extdata/empty_files/endoBam_empty.bam", 
                "extdata/empty_files/exoBam_empty.bam",
                "extdata/empty_files/wigfile_empty.bw", 
                "extdata/empty_files/wigfile_empty-RPM.bw"), 
        package="ChIPSeqSpike")

csds <- ChIPSeqSpikeDataset(
        endogenousBam_vec = c(file_vec[1], file_vec[1]), 
        exogenousBam_vec = c(file_vec[2], file_vec[2]), 
        bigWigFile_endogenous_vec = c(file_vec[3], file_vec[3]), 
        inputBigWigFile = file_vec[3], 
        inputBamFile = file_vec[1], 
        expnames = c("toto", "toto2"),
        inputSF = 0.7, inputNb = 1000)

csds2 <- ChIPSeqSpikeDataset(
        endogenousBam_vec = c(file_vec[1], file_vec[1]), 
        exogenousBam_vec = c(file_vec[2], file_vec[2]), 
        bigWigFile_endogenous_vec = c(file_vec[4], file_vec[3]), 
        inputBigWigFile = file_vec[3], 
        inputBamFile = file_vec[1], 
        expnames = c("toto", "toto2"),
        inputSF = 0.7, inputNb = 1000)

e1 <- Experiment(endogenousBamFilePath = file_vec[1], 
        exogenousBamFilePath = file_vec[2], 
        bigWigFilePath = file_vec[3], 
        name = "toto",
        endoScalingFactor = 1, exoScalingFactor = 2, 
        endoNb = 3, exoNb = 4)

e2 <- Experiment(endogenousBamFilePath = paste(indir, 
                list.files(indir)[7], sep="/"), 
        exogenousBamFilePath = file_vec[2], 
        bigWigFilePath = file_vec[3], 
        name = "toto",
        endoScalingFactor = 1, exoScalingFactor = 2, 
        endoNb = 3, exoNb = 4)


## Testing estimateScalingFactors and estimateScalingFactors_Experiment

context("Testing estimateScalingFactors")

test_that("Lack of aligned reads in bam files is handled", {
            
            expect_error(estimateScalingFactors(csds),
                    "input bam file contains no aligned reads.")
            
            expect_error(estimateScalingFactors(e1),
                    "Endogenous bam file contains no aligned reads.")
            
            expect_error(estimateScalingFactors(e2, paired=T),
                    "Exogenous bam file contains no aligned reads.")
            
        })


## Testing scaling and .computeScaling

context("Testing scaling and .computeScaling")

test_that("All parameters are valid", {
            
            if(.Platform$OS.type != 'windows') {
                
                expect_error(scaling(csds, outputFolder = "/toto/"),
                        "The specified output folder does not exist.")
                
                expect_error(scaling(csds, outputFolder = "./"),
                        "The path to the output folder should not end by '/'")
                
                expect_error(scaling(csds, type = "toto"),
                        "Accepted types are endo and exo.")
                
                expect_error(scaling(csds, reverse = TRUE, type = "exo"),
                        "Exogenous scaling factor cannot be reverted.")
                
                expect_error(scaling(csds, reverse = TRUE),
                     "RPM normalization must be performed before reverting it")
                
                expect_error(scaling(csds2, reverse = TRUE),
                        paste0("Input subtraction should be performed before ",
                                "reverting RPM normalization"))
                
                expect_error(scaling(csds, type = "exo"),
                        paste0("Exogenous scaling factor should be applied ",
                                "when RPM normalization has been reverted."))
            }
        })


## Testing inputSubtraction

context("Testing inputSubtraction")

test_that("Invalid data and differing number of chromosomes is not permitted", {
            
            if(.Platform$OS.type != 'windows') {
                
                expect_error(inputSubtraction(csds), 
                        paste0("RPM normalization must be performed before ",
                                "subtracting the input"))
            }
        })