tests/testthat/test-normalComparison.R

In KrasnitzLab/CNprep: Pre-process DNA Copy Number (CN) Data for Detection of CN Events

### Unit tests for normalComparison.R functions

library(CNprep)


### Tests normalComparison () results

context("normalComparison() results")



test_that("normalComparison() must return expected results 01", {
    
    normalmedian <- c(0.0230326977,  0.0069878681,  0.0013329618,  0.0110395179,  
                      0.0007606011,  0.0023178528, -0.0076653454, -0.0044130592, 
                      -0.0044268312, -0.0362319897)
    
    normalength <- c(11906049, 231977105,  86185990,   2411050, 151410255, 
                     199269234,  34587196,  60357381,  96145497,    620234)
    
    tumormad <- c(0.08502516, 0.13829131, 0.09701612, 0.12886650, 0.09179211, 
                  0.12066915, 0.09360264, 0.09505375, 0.12648441, 0.07690704)
    
    tumormedian <- c(0.046492091, -0.216771966,  0.041802329, -0.227213792,  
                     0.035899255,  0.243933069, -0.032015273, -0.004500177, 
                     -0.284767695, -0.010467050)
    
    tumorerror <- c(0.006267755, 0.009346934, 0.003025827, 0.006431545, 
                    0.003926070, 0.003544793, 0.002222607, 0.003353667, 
                    0.008923441, 0.012611398)
    
    tumorlength <- c(14912327,  21970269,  40526202,  24664080,  38759675, 
                     103077343, 102923669,  40349469,   8897435,   2210770)
    
    RNGkind("default")
    
    set.seed(222)
    
    results <- CNprep:::normalComparison(normalmedian = normalmedian, normalength = normalength, 
                                         tumormedian = tumormedian, 
                                         tumorlength = tumorlength, normalmad = NULL,
                                         normalerror = NULL, tumormad = tumormad,
                                         tumorerror = tumorerror)
                                             
    
    expected <- as.matrix(data.frame(samplesize=c(58, 39, 21, 35, 22, 8, 8, 21, 98, 395),
                           negtail=c(1.0000000000, 0.0000000000, 1.0000000000,
                                     0.0000000000, 1.0000000000, 1.0000000000,
                                     0.0007089442, 0.0402430422, 0.0000000000,
                                     0.0007089442)))
    
    expect_equal(results, expected)
})


test_that("normalComparison() must return expected results 02", {
    
    normalmedian <- c(0.0230326977,  0.0069878681,  0.0013329618,  0.0110395179,  
                      0.0007606011,  0.0023178528, -0.0076653454, -0.0044130592, 
                      -0.0044268312, -0.0362319897)
    
    normalmad <- c(0.05502516, 0.03829131, 0.05701612, 0.10886650, 0.06179211, 
                  0.02066915, 0.00360264, 0.03505375, 0.11648441, 0.07600704)
    
    normalength <- c(11906049, 231977105,  86185990,   2411050, 151410255, 
                     199269234,  34587196,  60357381,  96145497,    620234)
    
    tumormad <- c(0.08502516, 0.13829131, 0.09701612, 0.12886650, 0.09179211, 
                  0.12066915, 0.09360264, 0.09505375, 0.12648441, 0.07690704)
    
    tumormedian <- c(0.046492091, -0.216771966,  0.041802329, -0.227213792,  
                     0.035899255,  0.243933069, -0.032015273, -0.004500177, 
                     -0.284767695, -0.010467050)
    
    tumorerror <- c(0.006267755, 0.009346934, 0.003025827, 0.006431545, 
                    0.003926070, 0.003544793, 0.002222607, 0.003353667, 
                    0.008923441, 0.012611398)
    
    tumorlength <- c(14912327,  21970269,  40526202,  24664080,  38759675, 
                     103077343, 102923669,  40349469,   8897435,   2210770)
    
    RNGkind("default")
    
    set.seed(222)
    
    results <- CNprep:::normalComparison(normalmedian = normalmedian, normalength = normalength, 
                                         tumormedian = tumormedian, 
                                         tumorlength = tumorlength, normalmad = normalmad,
                                         normalerror = NULL, tumormad = tumormad,
                                         tumorerror = tumorerror)
    
    
    expected <- as.matrix(data.frame(samplesize=c(58, 39, 21, 35, 22, 8, 8, 21, 98, 395),
                                     negtail=c(1.0000000000, 0.0000000000, 1.0000000000,
                                               0.0000000000, 1.0000000000, 1.0000000000,
                                               0.0007089442, 0.0402430422, 0.0000000000,
                                               0.0007089442),
                                     negtailnormad=c(1.0000000000, 0.03953410, 1.0000000000,
                                                     0.03953410, 0.98639106, 1.00000000,
                                                     0.04024304, 0.10923316, 0.00000000,
                                                     0.04024304)))
    
    expect_equal(results, expected)
})


test_that("normalComparison() must return expected results 03", {
    
    normalmedian <- c(0.0230326977,  0.0069878681,  0.0013329618,  0.0110395179,  
                      0.0007606011,  0.0021178528, -0.0076653454)
    
    normalmad <- c(0.05202516, 0.03829131, 0.05701612, 0.10886650, 0.06179211, 
                   0.02066915, 0.00320264)
    
    
    normalerror <- c(0.000007755, 0.000346934, 0.000025827, 0.000431545, 
                    0.003026070, 0.000544793, 0.002200607)
    
    normalength <- c(11906049, 231577105,  86185990,   2111050, 151410255, 
                     199269234,  34587196)
    
    tumormad <- c(0.08602516, 0.13829131, 0.09701612, 0.12886650, 0.09179211, 
                  0.15066915, 0.09360264, 0.09505375, 0.12648441, 0.07690704)
    
    tumormedian <- c(0.049492091, -0.216771966,  0.041902329, -0.227213792,  
                     0.035899255,  0.243993069, -0.032015273, -0.004500177, 
                     -0.284767695, -0.010467050)
    
    tumorerror <- c(0.006267755, 0.009346934, 0.003025827, 0.006431545, 
                    0.003999070, 0.003544793, 0.092222607, 0.093353667, 
                    0.008923441, 0.012611398)
    
    tumorlength <- c(14912327,  2197069,  40526202,  24664080,  38759675, 
                     103077343, 102923669,  4034469,   8897435,   2210770)
    
    RNGkind("default")
    
    set.seed(212)
    
    results <- CNprep:::normalComparison(normalmedian = normalmedian, normalength = normalength, 
                                         tumormedian = tumormedian, 
                                         tumorlength = tumorlength, normalmad = normalmad,
                                         normalerror = normalerror, tumormad = tumormad,
                                         tumorerror = tumorerror)
    
    
    expected <- as.matrix(data.frame(samplesize=c(48, 326, 17, 29, 18, 6, 6, 177, 80, 324),
                                     negtail=c(1.0000000000, 0.0000000000, 1.0000000000,
                                               0.0000000000, 1.0000000000, 1.0000000000,
                                               0.00000000, 0.04823561, 0.0000000000,
                                               0.0000000000),
                                     negtailnormad=c(1.0000000000, 0.04823561, 0.98339572,
                                                     0.04823561, 0.98339572, 1.00000000,
                                                     0.04823561, 0.04823561, 0.04823561,
                                                     0.04823561),
                                     negtailnormerror=c(0.53729637, 0.00000000, 0.53729637,
                                                        0.00000000, 0.53729637, 0.98339572,
                                                        0.04823561, 0.04823561, 0.00000000,
                                                        0.04823561)))
    
    expect_equal(results, expected)
})