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Complex Question: Updating GroupList of AA's analyzed in ROC and or elsewhere #349

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mikegilchrist opened this issue Mar 12, 2020 · 1 comment

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@mikegilchrist
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For code development and testing purposes, I'd like to define a function that is accessible within R that restricts the list of AAs analyzed to a given subset, such as only 2 codon AA. Can Alex or Cedric provide me with some basic guidance or a 'todo' list?

@mikegilchrist
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Email from Cedric

There is a variable called groupList (defined in Parameter.h as a member of the base Parameter object).
Each type of parameter object (ROC, FONSE, …) then defines it’s own group list (AA, codons, …).
The group list defines how to group parameters, e.g. ROC looks at all synonymous codons at the same time while PANSE looks at individual codons.
For ROC that is done in ROCParameter.cpp (Line 79).

You have two options:

  • Expose the variable (groupList) to R which is done in RCPP_Parameter.cpp where each model specific parameter object (and the base object) expose
    their functions to R. Then write an R wrapper.
  • Maybe a better option is to add another constructor that requires to set the group list, then define a default for each model.

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