only zscore in meta outcome gwas summary data

[iamyingzhou]

Thanks for your wonderful work. I'm looking to conduct summary-stat-based association test on a meta-analysis GWAS. The output from the METAL software provides only the P-value and Z-score columns, without beta and standard error. Is it feasible to run association test with just the P-value and Z-score ?

[iamyingzhou]

I've just come to the realization that association tests using JIT pre-trained prediction models differ from the MR-JTI method. Is there a connection between the two?

Here is the code that I am using now Rscript ${src_dir}/predixcan_r.r \ --asso_test \ --db_path ${dir}/JTI_Liver.db \ --cov_path ${dir}/JTI_Liver.txt.gz \ --gwas_path ${dir}/LDLq.txt.gz \ --gwas_variant_col rsid \ --gwas_beta_col beta \ --gwas_se_col se \ --gwas_eff_allele_col eff_allele \ --gwas_ref_allele_col ref_allele \ --asso_out_path ${dir}/result_ldl_liver.txt \ --parallel

[zdangm]

Hi Yingzhou, Thanks for reaching out! predixcan_r.r --asso_test performs GReX-trait association test (the last step of TWAS), while MR-JTI is a Mendelian randomization test. For P+z-score, I'm afraid not. We recommend using beta+se. Dan

On Tue, Nov 28, 2023 at 11:12 PM Yingzhou Shi @.***> wrote:

I've just come to the realization that association tests using JIT pre-trained prediction models differ from the MR-JTI method. Is there a connection between the two?

Here is the code that I am using now Rscript ${src_dir}/predixcan_r.r \ --asso_test \ --db_path ${dir}/JTI_Liver.db \ --cov_path ${dir}/JTI_Liver.txt.gz \ --gwas_path ${dir}/LDLq.txt.gz \ --gwas_variant_col rsid \ --gwas_beta_col beta \ --gwas_se_col se \ --gwas_eff_allele_col eff_allele \ --gwas_ref_allele_col ref_allele \ --asso_out_path ${dir}/result_ldl_liver.txt \ --parallel

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