Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

issue in get_result.py #1

Open
MagicalLily opened this issue Nov 1, 2022 · 3 comments
Open

issue in get_result.py #1

MagicalLily opened this issue Nov 1, 2022 · 3 comments

Comments

@MagicalLily
Copy link

Hello, if the HLA allele of LossAllele column matches the HLA allele of HLA_A_type1 column, should the LOH be determined based on PVal_unique<0.01 and HLA_type1copyNum_withBAFBin < -1?

Best wishes!
Lily

@pyc1216
Copy link
Owner

pyc1216 commented Feb 13, 2023

Hello, Thank you for Pointing out the problem.
If LossAllele = HLA_A_type1, check HLA_type1copyNum_withBAFBin < -1, else check HLA_type2copyNum_withBAFBin. My script does not consider this situation. I will correct it later.

Best wishes!

@xiasijian
Copy link

image
I have no idea that you use log2.

@pyc1216
Copy link
Owner

pyc1216 commented Mar 27, 2024

image I have no idea that you use log2.

"You are right, log2 should not be used here. In some samples, HLA_type1copyNum_withBAFBin and HLA_type2copyNum_withBAFBin are calculated as negative numbers. I don't understand the reason for this, which was why I used log2 at that time."

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

3 participants