r^2 between SNPs on the NPR of the X-chromosome

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Zhiwen Jiang

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Apr 1, 2024, 11:12:51 AMApr 1
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Dear FUMA team,
How did you calculate the r^2 (squred correlation coefficient) between SNPs on the NPR of the X-chromosome? Did you use only females or males and females combined? If the latter case, what was the coding scheme for males (i.e., 0 1, or 0 2) ?

Best,
Owen

fuma.ctglab

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Apr 3, 2024, 5:31:13 PMApr 3
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Dear Owen, 

Thank you for your message. We will need some time to look into this. 
Thank you for your patience. 

Marijn Schipper

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Apr 9, 2024, 5:40:03 AMApr 9
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Ld calculation was performed using the following plink command:
PLINK (--r2 --ld-window 99999 --ld-window-r2 0.05) On the 1000Genomes plink files, without sex encoding.

Please let me know if you have any further questions.

Best,

Marijn

Op woensdag 3 april 2024 om 23:31:13 UTC+2 schreef fuma.ctglab:
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