JonJala
"GWAS mean chi^2" not shown
Hi, I have run mtag successfully. However, my results of "GWAS mean chi^2" are omitted in the log file. It does say there are 7 columns, but three columns including "GWAS mean chi^2" are missing. Do you know how to see the full Table?
Or, the tutorial says "The GWAS mean chi^2 column is adjusted by the diagonal terms of Sigma." Do you know how to calculate the adjusted "GWAS mean chi^2" using Sigma? Thank you so much!
Summary of MTAG results:
Trait # SNPs used ... MTAG mean chi^2 GWAS equiv. (max) N
1 ta.sum 7553766 ... 1.528 647814
2 te.sum 7553766 ... 1.529 223038
[2 rows x 7 columns]
Estimated Omega: [[ 1.345e-05 -6.030e-06] [-6.030e-06 2.759e-06]]
(Correlation): [[ 1. -0.99] [-0.99 1. ]]
Estimated Sigma: [[0.972 0.116] [0.116 1.011]]
(Correlation): [[1. 0.117] [0.117 1. ]]
MTAG weight factors: (average across SNPs) [-0.804 0.371]
I solved this by renaming the 7 columns with shorter names in the mtag.py script.
The latest commit (as of today) has a change that should allow the whole summary table to print. If you try that out, let us know? (if you have any issues or problems, we'll fix that or revert, and if it works as intended, that's also good to know).
On Sat, Aug 13, 2022 at 11:47 PM xchangchop @.***> wrote:
I solved this by renaming the 7 columns with shorter names in the mtag.py script.
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