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fhormoz / caviar

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question about the direction of z-score ,beta for A1/A2 and the ld matrix r #27

Open EchoLee0925 opened 2 years ago

EchoLee0925 commented 2 years ago

Whether the positive and negative sign of beta for A1/A2, z-score and ld matrix r effect the PIP? Is there to harmonise the orientation?

fhormoz commented 2 years ago

The sign of Z-score and LD matrix matter. They both need to use the same effect allele to compute the Z-score and the LD matrix. You can use the PLINK to create the LD matrix. Please be aware that PLINK ordering of variants is based on the BIM file and not your input ordering. In addition, you have to make sure the LD and Z-score have the same oder of variants.