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Calculate dN and dS by counting fixations #64

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ebrintn opened this issue Mar 3, 2023 · 7 comments
Open

Calculate dN and dS by counting fixations #64

ebrintn opened this issue Mar 3, 2023 · 7 comments

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@ebrintn
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ebrintn commented Mar 3, 2023

Use fixation counting commands to calculate dN and dS
ebrintn added a commit that referenced this issue Mar 3, 2023
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implemented function for countind dN and dS - iss #64
354ca42
ebrintn added a commit that referenced this issue Mar 3, 2023
@ebrintn
implemented function for countind dN and dS - iss #64
f1ac4c4
ebrintn added a commit that referenced this issue Mar 3, 2023
@ebrintn
fixed bug in dn ds for iss #64
0356014
ebrintn added a commit that referenced this issue Jun 2, 2023
@ebrintn
Fixed bugs in dN/dS measurement for the computer version of slim-tree…
e7ad466 
… (iss #64), I will hopefully have the HPC version done tonight!
ebrintn added a commit that referenced this issue Jun 2, 2023
@ebrintn
Fixed the dN/dS measurement for slim-tree hpc (iss #64)
6ee95ff
ebrintn added a commit that referenced this issue Jun 2, 2023
@ebrintn
Fixed bug in dN/dS calculation - this should theorectically work beca…
efdb905 
…use I tested in redev - iss #64
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ebrintn commented Jun 2, 2023

Should be working now - @afarineshp can you check to see if you are getting the error you were getting before?

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ebrintn commented Jun 15, 2023

Fixed all bugs - see iss #37. Closing.

@ebrintn ebrintn closed this as completed Jun 15, 2023
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ebrintn commented Jun 25, 2023

Talked in meeting about needing to add denominators from stationary distributions.

These values are really weird when implemented. I think we need to meet and talk more.

@ebrintn ebrintn reopened this Jun 26, 2023
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ebrintn commented Jun 26, 2023

Not all codon distributions will be the same. Change to have users specify codon stationary distributions instead.

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ebrintn commented Sep 4, 2023

Updated with most recent push to include mutation matrices!

@ebrintn ebrintn closed this as completed Sep 4, 2023
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ebrintn commented Mar 21, 2024

Counted each value of dN/dS and output the specific substitutions. Users can now see the denominators. I also fixed a bug in the way that fixations are determined. This may change the way that we were seeing substitutions before.

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ebrintn commented Mar 22, 2024

I definately think that it needs to be multiplied not divided by the selection coefficient we calculated

@ebrintn ebrintn reopened this Mar 22, 2024
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