Kijoung Song

ERROR converting summary statistics

25

Hi there, I got the ValueError like below when I ran the following; python mtag-master/mtag.py --sumstats data1.txt,data2.txt --p_name pval_raw --out mtag-master/OA_chr --use_beta_se --beta_name beta --se_name se --n_min 0.0 --stream_stdout We...

Unkown error

12

Hi all, I ran MTAG for 2 traits. Trait 2 was categorical. I met the error after Merge of GWAS summary statistics complete. Please see the below and advise me;...

Conditional analysis based on MTAG results

1

Hi, I'd like to hear your opinion in terms of this concern. One of my colleagues brought the following up. "GCTA-COJO computes an estimate of the phenotypic variance by looking...

Discrepancy between LDSC and MTAG

1

Hi, I found a huge discrepancy in the genetic correlation & mean of chi^2 between LDSC and MTAG. LDSC = 0.47 vs. MTAG = 0.27 Do you have any idea?...

Two questions

4

1. I have case-control GWAS summary statistics that do not have the N-columns. How to define 'N'? Should I use N-cases or N-total to define 'N' ? 2. Can I...

Genetic correlation before/after

1

Hi, I ran MTAG with two traits (data1=better power, but less specific, data2=less power, but more specific). The genetic correlation of both gwas results was 62% (p=1.8e-47). However, after mtag...

The huge discrepancy between z_mtag and z_gwas

2

I expected that Z_mtag and Z_gwas are near perfect fit like the mtag paper. However, my results showed that there is a huge discrepancy between z_mtag and z_gwas as below....

gwas lambda inflation factor

1

Hi there, Recently, I combined 4 different traits using MTAG without any error or warning. However, I concern about the lambda inflation factor because the lambda is higher than expected....