Possible Error in Selecting the pool cutoff function

[Saiteja-Reddy]

In the gene pool cutoff function here, why is the cumulative sum being subtracted from 1?

As per the paper we must be implementing this,

So, I am guessing the subtraction from one must be removed, or is it actually implemented correctly ?

Thanks.

[emreg00]

Dear Sai Teja, Thanks for your comment, the idea is to find the number of subjects Xrand per gene that is expected according to the random model. We check P(x>=X), the probability of a gene appearing at least in X samples (thus the cumulative probability distribution), calculate the probability of not seeing a gene across X or more samples (thus 1 minus) and choose the largest X that would violate random expectation (min in function as the values are ordered in descending order from lowest to highest X). Hope this helps, Emre

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On Tue, Mar 26, 2019 at 7:52 AM Sai Teja Reddy Moolamalla < ***@***.***> wrote: In the gene pool cutoff function here <https://github.com/emreg00/pepper/blob/master/classify_simple.R#L241>, why is the cumulative sum being subtracted from 1? As per the paper we must be implementing this, <https://user-images.githubusercontent.com/16854126/54976672-128ca380-4fc1-11e9-9863-cd44292c2485.png> So, I am guessing the subtraction from one must be removed, or is it actually implemented correctly ? Thanks. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADFqlSEbStT16hF0eLcAde8To8f9F7uPks5vacOPgaJpZM4cKuHw> .