Typo in PLINK PRS calculation

[williamthistle]

I believe there's a typo in the tutorial found here:

https://choishingwan.github.io/PRS-Tutorial/plink/

To calculate PRS, the following command is provided:

plink \ --bfile EUR.QC \ --score Height.QC.Transformed 3 4 12 header \ --q-score-range range_list SNP.pvalue \ --extract EUR.valid.snp \ --out EUR

This produced an error on my end because there aren't 12 columns in the Height.QC.Transformed file (only 11). I think the --score argument should instead be "Height.QC.Transformed 3 4 9 header" (since the OR column is 9th). Also, in the description of the parameters below the command, the value "Height.QC.Transformed 3 4 11 header" is given in the table (should read 3 4 9?), and the description of that parameter value states "the 12th column is the effect size estimate" (I think this should read 9th).

Also, minor point, but "Parameter" is misspelled in the first column header :)

Thanks for the excellent introduction to PRS!

[choishingwan]

Thanks, that was indeed a typo. It should've been 3 4 12 in the table with our latest data.

Also, thanks for spotting the spelling mistake.

On Mon, Aug 3, 2020 at 1:24 PM William Thistlethwaite < notifications@github.com> wrote:

I believe there's a typo in the tutorial found here:

https://choishingwan.github.io/PRS-Tutorial/plink/

To calculate PRS, the following command is provided:

plink --bfile EUR.QC --score Height.QC.Transformed 3 4 12 header --q-score-range range_list SNP.pvalue --extract EUR.valid.snp --out EUR

I think the --score argument should instead be "Height.QC.Transformed 3 4 11 header". In the description of the parameters below the command, the correct value "Height.QC.Transformed 3 4 11 header" is given in the table, but the description of that parameter value erroneously states "the 12th column is the effect size estimate" (I think this should read 11th).

Also, minor point, but "Parameter" is misspelled in the first column header :)

Thanks for the excellent introduction to PRS!

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[williamthistle]

Thanks! Quick follow-up question - where is the latest data? On the page here:

https://choishingwan.github.io/PRS-Tutorial/base/

I clicked the Google Drive link to download the summary statistic file (found at the top of the page):

https://drive.google.com/file/d/1RWjk49QNZj9zvJHc9X_wyZ51fdy6xQjv/view?usp=sharing

But this file has 11 columns. Is this the old version of the data?

[choishingwan]

You get the 12 th column by following the tutorial

On Tue, 4 Aug 2020 at 4:39 AM, William Thistlethwaite < notifications@github.com> wrote:

Thanks! Quick follow-up question - where is the latest data? On the page here:

https://choishingwan.github.io/PRS-Tutorial/base/

I clicked the Google Drive link to download the summary statistic file (found at the top of the page):

https://drive.google.com/file/d/1RWjk49QNZj9zvJHc9X_wyZ51fdy6xQjv/view?usp=sharing

But this file has 11 columns. Is this the old version of the data?

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