add tests for d-ratio to check it filters as expected and computes the ratio correctly
Gavin Rhys Lloyd authored on 10/07/2023 11:04:38
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+# filter d-ratio |
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+test_that('d-ratio filter works as expected',{
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+ set.seed('57475')
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+ # DatasetExperiment |
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+ DE = MTBLS79_DatasetExperiment(filtered=TRUE) |
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+ M = dratio_filter( |
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+ threshold=20, |
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+ qc_label = 'QC', |
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+ factor_name='Class' |
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+ ) |
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+ M = model_apply(M,DE) |
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+ |
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+ # manually compute d-ratio |
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+ qc_mad=unlist( |
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+ lapply(DE$data[DE$sample_meta$Class=='QC',],mad,na.rm=TRUE) |
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+ ) |
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+ sa_mad=unlist( |
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+ lapply(DE$data[DE$sample_meta$Class!='QC',],mad,na.rm=TRUE) |
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+ ) |
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+ dr = (qc_mad/(qc_mad+sa_mad))*100 |
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+ |
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+ # check manual vs fcn |
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+ expect_true(all(dr==M$d_ratio$d_ratio)) |
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+ |
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+ # check values havent changed |
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+ expect_equal(dr[[1]],12.39,tolerance = 1e3) |
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+ expect_equal(dr[[100]],32.54,tolerance = 1e3) |
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+ |
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+ # just number of filtered columns |
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+ expect_true(ncol(predicted(M))==1052) |
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+ expect_true(ncol(DE)-ncol(predicted(M))==527) |
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+ expect_true(ncol(DE)-ncol(predicted(M))==sum(dr>20)) |
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+}) |