consolidate observedMutations

[ssnn]

Similar to issue #141. Refactor, and have one observedMutations function that can reproduce previous behavior and also work with the extended region definition.

[ssnn]

3859716

[ssnn]

@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.

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>     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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