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choishingwan / PRS-Tutorial

A tutorial on how to run basic polygenic risk score analysis
MIT License
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a typo? map <- obj.bigSNP$map[-2] #14

Closed XcodeBio closed 3 years ago

XcodeBio commented 3 years ago

Hi Sam,

Thank you very much for the wonderful PRS tutorial. It is very helpful.

I was going through your LDpred-2 tutorial and I there might be a typo in section 3 ("Reformat data in preparation of LDpred2").

extract the SNP information from the genotype

map <- obj.bigSNP$map[-2]

Should this be: map <- obj.bigSNP$map[-3]

Thanks

choishingwan commented 3 years ago

You are correct. I think there might have been a version change to bigsnpr which changes some of the data structure. Will try to update this part of the tutorial now.

On Wed, Nov 4, 2020 at 10:29 AM XcodeBio notifications@github.com wrote:

Hi Sam,

Thank you very much for the wonderful PRS tutorial. It is very helpful.

I was going through your LDpred-2 tutorial and I there might be a typo in section 3 ("Reformat data in preparation of LDpred2"). extract the SNP information from the genotype

map <- obj.bigSNP$map[-2]

Should this be: map <- obj.bigSNP$map[-3]

Thanks

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XcodeBio commented 3 years ago

Thank you!