KING Discussions
Not logged in [Login - Register]
Go To Bottom

Printable Version  
Author: Subject: PCA on EUR subpopulation

Posts: 1
Registered: 2/3/2023
Member Is Offline

[*] posted on 2/3/2023 at 04:24 AM
PCA on EUR subpopulation


I would like to use king on my GWAS dataset in order to do ancetry inference using 1KG subpopulation (GBR, CEU, FIN, CDX, KHV, etc..). How do I force the --pca --projection to use a homemade 1KG_popref.txt file?
Is there anyway to do that?
Many thanks

example... head of the file
FID IID Population
HG00096 HG00096 GBR
HG00097 HG00097 GBR
HG00099 HG00099 GBR
HG00100 HG00100 GBR
HG00101 HG00101 GBR
HG00102 HG00102 GBR
HG00103 HG00103 GBR
HG00105 HG00105 GBR
HG00106 HG00106 GBR
View user's profile View All Posts By User

  Go To Top

Powered by XMB 1.9.12
XMB Forum Software © 2001-2021 The XMB Group
[Queries: 16] [PHP: 55.9% - SQL: 44.1%]