Under "example summary statistics" for load summary, you specify "a1" as reference or coding allele, "a2" as alternate, "freq" as "allele frequency", "beta" as effect sizes, etc. Later in section titled "multitraits correlation replication", you reference load.summary function ("all data required is available in outputs of load.summary"). Now you specify under data required: "A1" as effect allele, "A2" as reference allele", etc.
So my question, for load summary, do you mean "a1" to be effect allele (so "beta" would be effect size for a1, and "freq" would. be effect allele frequency)? Reference allele do. not seem to always be the effect allele (allele for which effect size is calculated for GWAS): in the Neale Lab UKBB GWASs, for example, the "effect allele" is always the "alternate allele" ie not the "reference allele".
Thanks in advance for your clarification!
Under "example summary statistics" for load summary, you specify "a1" as reference or coding allele, "a2" as alternate, "freq" as "allele frequency", "beta" as effect sizes, etc. Later in section titled "multitraits correlation replication", you reference load.summary function ("all data required is available in outputs of load.summary"). Now you specify under data required: "A1" as effect allele, "A2" as reference allele", etc.
So my question, for load summary, do you mean "a1" to be effect allele (so "beta" would be effect size for a1, and "freq" would. be effect allele frequency)? Reference allele do. not seem to always be the effect allele (allele for which effect size is calculated for GWAS): in the Neale Lab UKBB GWASs, for example, the "effect allele" is always the "alternate allele" ie not the "reference allele".
Thanks in advance for your clarification!