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Incorrect external neighbors when using reverse complements #9

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fkhalid opened this Issue Dec 12, 2016 · 1 comment

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fkhalid commented Dec 12, 2016

For a genotype g_1 in a genotype set G_1, all 1-mutants of g_1 that do not lie in G_1, a.k.a external neighbors, are generated for several different analyses. The generation/computation of such 1-mutants is at present not correct when the '-rc' flag is used.

A correct implementation is required for accurate results of analyses like Evolvability, Accessibility, Neighbor abundance, Diversity index, etc.

@fkhalid fkhalid self-assigned this Dec 12, 2016

@fkhalid fkhalid added the bug label Dec 12, 2016

@fkhalid fkhalid closed this in 77bc09c Dec 16, 2016

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fkhalid Dec 16, 2016

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The following holds true only when reverse complements are considered, which is currently only possible when working with DNA genotypes.

Let g_1 be a genotype in the genotype network G_1.

Let neighbors_external be the set of all 1-mutants of g_1 that do not exist in G_1.

Then when generating external neighbors for all genotypes in G_1, it is now ensured that the list of external neighbors consists only of unique gentoypes that do not exist in G_1. This means, that either a genotype or its reverse complement can be in the list of external neighbors, but not both. Further checks ensure that all special cases are handled properly.

The impact of this change is higher on genotype level results, but minimal on genotype set level results.

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fkhalid commented Dec 16, 2016

The following holds true only when reverse complements are considered, which is currently only possible when working with DNA genotypes.

Let g_1 be a genotype in the genotype network G_1.

Let neighbors_external be the set of all 1-mutants of g_1 that do not exist in G_1.

Then when generating external neighbors for all genotypes in G_1, it is now ensured that the list of external neighbors consists only of unique gentoypes that do not exist in G_1. This means, that either a genotype or its reverse complement can be in the list of external neighbors, but not both. Further checks ensure that all special cases are handled properly.

The impact of this change is higher on genotype level results, but minimal on genotype set level results.

fkhalid added a commit that referenced this issue Jan 20, 2017

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