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choishingwan / PRS-Tutorial

A tutorial on how to run basic polygenic risk score analysis
MIT License
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plink parameters for generating PRS #13

Open xcliu-oc opened 3 years ago

xcliu-oc commented 3 years ago

Thank you for creating this tutorial!

when I run plink code you 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

there are only 11 columns in Heitght.QC.Transformed, shown below: CHR BP SNP A1 A2 N SE P OR INFO MAF 1 1 756604 rs3131962 A G 388028 0.00301666 0.483171 -0.00211532 0.8905579 0.3693896 2 1 768448 rs12562034 A G 388028 0.00329472 0.834808 0.00068708 0.8958935 0.3368458 3 1 779322 rs4040617 G A 388028 0.00303344 0.428970 -0.00239932 0.8975083 0.3773680 4 1 801536 rs79373928 G T 388028 0.00841324 0.808999 0.00203363 0.9089629 0.4832122 5 1 808631 rs11240779 G A 388028 0.00242821 0.590265 0.00130747 0.8932125 0.4504096 6 1 809876 rs57181708 G A 388028 0.00336785 0.714750 0.00123090 0.9235576 0.4997439

is the code should be --score Height.QC.Transformed 3 4 **9** header \, sicne column 9 is the log-transformed OR?

Thanks

choishingwan commented 3 years ago

Hi,

You should have 12 columns, where the 12th column is named BETA

(Maybe you are referring to an older version of the tutorial where for the non-data.table option, I forgot to make a new column but instead replaced the OR column)

Sam

xcliu-oc commented 3 years ago

Hi, You should have 12 columns, where the 12th column is named BETA (Maybe you are referring to an older version of the tutorial where for the non-data.table option, I forgot to make a new column but instead replaced the OR column) Sam

yes, I saw the BETA column in the with data.table option. Thanks for confirming it, i will go ahead use column 9, as they should be the same