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choishingwan / PRS-Tutorial

A tutorial on how to run basic polygenic risk score analysis
MIT License
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Typo in "Update Effect Size" subsection in the section PLINK #11

Closed MapleHe closed 3 years ago

MapleHe commented 3 years ago

Hello developer/researcher, thank you for your excellent Tutorial.

In the "update effect size" section of the tutorial, the R code in "Without data.table" just overwrites the 9th "OR" column instead of generating the 11th "BETA" column. This is different from the R code in "With data.table" and will cause the following error in PRS-calculating step.

Error: Line 2 of --score file has fewer tokens than expected.
choishingwan commented 3 years ago

Oh, that line should be

dat$Beta<- log(dat$OR)

On Sun, 18 Oct 2020 at 10:01 PM, MapleHe notifications@github.com wrote:

Hello developer/researcher, thank you for your excellent Tutorial.

In the "update effect size" section https://choishingwan.github.io/PRS-Tutorial/plink/#update-effect-size of the tutorial, the R code in "Without data.table" just overwrites the 9th "OR" column instead of generating the 11th "BETA" column. This is different from the R code in "With data.table" and will cause the following error in PRS-calculating step.

Error: Line 2 of --score file has fewer tokens than expected.

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-- Dr Shing Wan Choi Postdoctoral Fellow Genetics and Genomic Sciences Icahn School of Medicine, Mount Sinai, NYC

MapleHe commented 3 years ago

Thank you for your response.