Calculating polygenic score using plink
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7 weeks ago
m.shoaib • 0

Hi I am trying to calculate PRS in test sample after getting best SNPs from PRSice 2 with highest R2 My target data is in the form of bed,bim, fam for 22 chromosomes, I want to use plink for specific p-value threshold in this scenerio,

plink2 \

--bfile T2test3 \                            ## For one chromosme only

--score T2baseNoBMI.uniq.txt 2 4 6 header \

--q-score-range range_list SNP.pvalue \

--extract EUR.valid.snp \

--out EUR


This is working for just a single chromosome, I want to perform my analysis considering all autosomes and need a final final file with IIDs and their corresponding PRS based on all chromosome SNP information,

Please help

Thanks

Plink 2 scores UKBB PRSice • 443 views
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Entering edit mode
7 weeks ago
Sam ★ 4.2k

You will need to combine the genotype file. Not sure if --score works with --bmerge. You can have a try.

Alternatively, as you are already using PRSice, do

--bar-levels <p-value threshold> --no-full --fastscore and you should in theory get the PRS at the specific p-value threshold

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Ok. PRSice seems more convenient for me at this stage. So, In order to calculate the PRS in my test data, can I simply provide, GWAS base data, target data with these options, -bar-levels <p-value threshold> --no-full --fastscore? I cannot provide phenotype file because my independent sample comprised of 3 different phenotypic categories and I simply need to calculate the PRS at the specific threshold for specific individuals. I donot need bar plot and models with R2. Thanks

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if you don't need the plots or R2, then add in --no-regress

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Thank you very much for your response!

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