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dekoning-lab / slim-tree

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Calculate dN and dS by counting fixations #64

Closed ebrintn closed 1 week ago

ebrintn commented 1 year ago

Use fixation counting commands to calculate dN and dS

ebrintn commented 1 year ago

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

ebrintn commented 1 year ago

Fixed all bugs - see iss #37. Closing.

ebrintn commented 1 year ago

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 commented 1 year ago

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

ebrintn commented 1 year ago

Updated with most recent push to include mutation matrices!

ebrintn commented 8 months ago

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.

ebrintn commented 8 months ago

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

ebrintn commented 1 week ago

I started thinking about this again and I realize where I was wrong last time - the denominator of the dN/dS values should be individual. I will fix today

ebrintn commented 1 week ago

Talked with @jasondk and this is correct except we need to multiply by 3 instead of divide.