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JTNelsonWSU / COMICS

ICS pipeline for genomic data using COMICS
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Meaning of 'First' and 'Second' Indexes. #4

Open javibio-git opened 3 years ago

javibio-git commented 3 years ago

Hi, I just came across this interesting implementation of the ICS method and want to use it for my popgen data. I am generating outputs from SweeD, omegaplus and xpclr but first I am giving it a try with the toy data included in this repository.

Once the app is running, I feel everything is pretty self-explanatory except for the 'First index' and 'Second index'. Could elaborate more on what those parameter mean and how they affect the output?

Looking forward to hearing back from you.

Javier,

JTNelsonWSU commented 3 years ago

Hey Javier,

Thanks for reaching out! The first and second index refer to the invariant coordinates that are being used. In the case of multi-dimensional data, the number of invariant coordinates equals the number of selection scans you are using. It's like a PCA, where each invariant coordinate (first, second, third, .... nth index) is like a principal component.

Let me know if you have any additional questions.

Joel Nelson, PhD Washington State University | Department of Biological Sciences Office: 429 Heald Phone: 443-417-7720 Email: @.***

From: Javier Carpinteyro-Ponce @.> Sent: Tuesday, July 27, 2021 2:11 PM To: JTNelsonWSU/COMICS @.> Cc: Subscribed @.***> Subject: [JTNelsonWSU/COMICS] Meaning of 'First' and 'Second' Indexes. (#4)

Hi, I just came across this interesting implementation of the ICS method and want to use it for my popgen data. I am generating outputs from SweeD, omegaplus and xpclr but first I am giving it a try with the toy data included in this repository.

Once the app is running, I feel everything is pretty self-explanatory except for the 'First index' and 'Second index'. Could elaborate more on what those parameter mean and how they affect the output?

Looking forward to hearing back from you.

Javier,

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javibio-git commented 3 years ago

Hi Joel

Thank you for the clarification.

Yes, I have one more question. For the 'genome.scans' file, it is just the list of likelihoods calculated by sweed, omegaplus and xpclr for each window for each chromosome, right?

Best,

Javier