Re: effect/other allele #258
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Hello, I'm calculating the PGS of the genome input files (bfiles) from our GWAS data with the PGS002814 score file. PGS002814 score file Our bim file Is it possible that the score was summed up in the opposite direction? If so, is there any way to adjust this? |
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Replies: 1 comment
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The difference in REF/ALT orientation shouldn't matter in this case, pgsc_calc (plink underlying) will count the dosage of the effect allele G and use it to calculate the score. It is sometimes possible that the authors provide the PGS Catalog scoring files where the alleles are swapped or weights reversed which can yield a PRS that is anti-correlated with your trait, it might simply be that. |
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The difference in REF/ALT orientation shouldn't matter in this case, pgsc_calc (plink underlying) will count the dosage of the effect allele G and use it to calculate the score. It is sometimes possible that the authors provide the PGS Catalog scoring files where the alleles are swapped or weights reversed which can yield a PRS that is anti-correlated with your trait, it might simply be that.