PRS-Tutorial

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Trying to work through the tutorial but cannot get the base data file. The `Base data` link on https://choishingwan.github.io/PRS-Tutorial/ under the heading "Datasets" just links to the QC of base...

AlexKoeppelSigSci

LD-pred 2 issue, All NAs in PRS file

1

Hi Sam, I am using LD pred 2 and used this tutorial, https://choishingwan.github.io/PRS-Tutorial/ldpred/ Actually, I have run the entire code with no errors but at the last step, where it...

ShoaibBME

ShoaibBME

Question on PRSice-2 section results & documentation

7

Hi and first of all thank you for your excellent paper/tutorial and documentation on conducting PRS analyses. I am having an issue replicating one of the results in the [PRSice-2...

james16292

The PRS. best file is shown to report all samples(n>1000) but the report says only 217 samples were included in the analysis; this was on purpose with the log message...

SamGreen52

Is there any possible way to check which SNPs is included in counting the score of the scoring profile? any flag to put in the PLINK command line?

fzel1994

#mismatching-snps

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Hi Sam, I am following your plink PRS tutorial and I have a couple of questions re mismatching-snps section [https://choishingwan.github.io/PRS-Tutorial/target/#mismatching-snps](url) . 1. You say in the 'Note' section that 'Most...

DM087

Error in calculating LD

5

I got the error below when it was calculating LD. I try to figure it out, but I can't even tell what the error message means. My R code for...

Qiaolan

'ind.col' and 'rows_along(A.col)' should have the same length.

1

```R pred_grid

Sandyyy123

Not able to reproduce the best fit PRS for plink

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Hi Sam, Thanks for the great tutorial. I have been trying PLINK for the polygenic risk score. However, with the height dataset and EUR plink files, I am not able...

ranijames