- edited description
consolidate observedMutations
Issue #143
resolved
Similar to issue #141. Refactor, and have one observedMutations
function that can reproduce previous behavior and also work with the extended region definition.
Comments (5)
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reporter -
reporter - changed status to open
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reporter - changed milestone to next release
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reporter - changed status to resolved
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reporter @milca tarshish Please, review this test that fails, and that I have commented out: https://bitbucket.org/kleinstein/shazam/src/802de4a6d5ec328da240e231b9fd57243c592124/tests/testthat/test_MutationProfiling.R#lines-2797:2798
It didn’t fail before, because tolerance was set to
tolerance=001
. After changing to `tolerance=0.001`, the test fails. Maybe increasing the tolerance is fine, but given that you wrote the extended region definitions code and tests, I think it is better if you review and decide what to do with this.
> expect_equal(db_exp_ALL_REGIONS[,columns_V_REGIONS]/(sum_db_exp_ALL_REGIONS_FWR123 + sum_db_exp_ALL_REGIONS_CDR12), + as.data.frame(db_exp_V_BY_REGIONS[,columns_V_REGIONS]), tolerance=0.001) Error: `/`(...) not equal to as.data.frame(db_exp_V_BY_REGIONS[, columns_V_REGIONS]). Component “mu_expected_cdr1_r”: Mean relative difference: 0.001583764 Component “mu_expected_cdr1_s”: Mean relative difference: 0.001546665 Component “mu_expected_cdr2_r”: Mean relative difference: 0.001754587 Component “mu_expected_cdr2_s”: Mean relative difference: 0.001623871 Component “mu_expected_fwr1_r”: Mean relative difference: 0.001781604 Component “mu_expected_fwr1_s”: Mean relative difference: 0.001834398 Component “mu_expected_fwr2_r”: Mean relative difference: 0.001842687 Component “mu_expected_fwr2_s”: Mean relative difference: 0.001642512 Component “mu_expected_fwr3_r”: Mean relative difference: 0.003116085 > db_exp_ALL_REGIONS[,columns_V_REGIONS]/(sum_db_exp_ALL_REGIONS_FWR123 + sum_db_exp_ALL_REGIONS_CDR12) mu_expected_cdr1_r mu_expected_cdr1_s mu_expected_cdr2_r mu_expected_cdr2_s mu_expected_fwr1_r mu_expected_fwr1_s mu_expected_fwr2_r mu_expected_fwr2_s mu_expected_fwr3_r 1 0.08048343 0.02716326 0.08497478 0.02749054 0.1509590 0.04758562 0.09448658 0.04299707 0.3306399 2 0.07322220 0.01489869 0.12468894 0.02770002 0.1528349 0.05491810 0.11517210 0.03268472 0.3209418 3 0.06886640 0.01817383 0.11079264 0.02572712 0.1647904 0.05839042 0.12033662 0.03595305 0.3042487 mu_expected_fwr3_s 1 0.11321979 2 0.08293850 3 0.09272084 > as.data.frame(db_exp_V_BY_REGIONS[,columns_V_REGIONS]) mu_expected_cdr1_r mu_expected_cdr1_s mu_expected_cdr2_r mu_expected_cdr2_s mu_expected_fwr1_r mu_expected_fwr1_s mu_expected_fwr2_r mu_expected_fwr2_s mu_expected_fwr3_r 1 0.08047289 0.02715971 0.08496365 0.02748694 0.1509392 0.04757938 0.09447421 0.04299144 0.3301240 2 0.07321167 0.01489655 0.12467101 0.02769603 0.1528129 0.05491020 0.11515554 0.03268002 0.3203767 3 0.06919783 0.01826129 0.11132585 0.02585093 0.1655835 0.05867144 0.12091577 0.03612608 0.3023514 mu_expected_fwr3_s 1 0.11380857 2 0.08358936 3 0.09171599
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