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Robustness analysis with reverse complements is inaccurate #10

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fkhalid opened this Issue Jan 19, 2017 · 1 comment

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fkhalid commented Jan 19, 2017

As per the current implementation, the same algorithm is used for the calculation of genotype robustness, regardless of whether or not reverse complements should be considered.

When calculating genotype robustness with the -rc or the --use_reverse_complements flags, the following additional checks are required:

  1. If the reverse complement of genotype g1 is also a 1-mutant of g1, it should not be included in the list of all possible 1-mutants of g1.
  2. For a genotype gn in the list of all possible 1-mutants of a genotype g1, either gn or the reverse complement of gn should be included, but not both.

Since the checks described above are not currently implemented, the denominator in genotype robustness calculation can be larger than it should be. Therefore, the above checks should be implemented for accurate calculation of genotype robustness values.

@fkhalid fkhalid added the bug label Jan 19, 2017

@fkhalid fkhalid self-assigned this Jan 19, 2017

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fkhalid Jan 20, 2017

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The bug highlighted in this issue has been fixed as per the provided suggestions. The issue was resolved with commit af60149.

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fkhalid commented Jan 20, 2017

The bug highlighted in this issue has been fixed as per the provided suggestions. The issue was resolved with commit af60149.

@fkhalid fkhalid closed this Jan 20, 2017

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