Merge Score in plink

Question

[Sumeet]

Hello,

I have generated a posterior effect size estimate for each SNP using the PRScs.As they mentioned in their manual, 'PRS can be generated by using PLINK.' Hence, I have generated PRS using plink. But, separate scores are generated for each chromosome. So, I wondered if there is any method to combine scores from all chromosomes?

Answer 1

[Sam]

You can combine the effect size estimates from PRScs into one single files to calculate the genome wide scores. If your genotype files are separated into different chromosome, then make sure you calculate the scores with no-sum modifier, then you can just add up the scores of each individual across all chromosome

[Sumeet]

Thank you.

[khn]

I think you do not need to calculate the scores with no-sum, though I agree with adding up the scores of each individual across all chromosome

[Sam]

FYI, without no-sum, the PRS is actually $sum ( beta * geno) / num allele$. The denominator will cause problem when you add up the score.

[khn]

Thank you for your comment. I understand it very well.