maxFDR of one single trait is over 0.05

[SuzyCC719]

Hi Patrick,

I have some issues when running MTAG. When I calculated maxFDR with 5 traits, the maxFDR for trait 5 was around 0.057. Could you please help me with interpreting these results? Is it suitable to use MTAG for these five traits?

The summary of MTAG results was listed below: Trait # SNPs used N (max) N (mean) GWAS mean chi^2 MTAG mean chi^2 GWAS equiv. (max) N 1 .../1_MTAG.txt 7169289 29006 21321 1.617 1.619 29104
2 ...2_MTAG.txt 7169289 1165720 1147707 1.625 1.662 1234512
3 ...3_MTAG.txt 7169289 964057 931789 1.132 1.319 2324005
4 ...4_MTAG.txt 7169289 471717 471717 1.205 1.571 1314393
5 ...5_MTAG.txt 7169289 278024 278024 1.114 1.229 557948

Estimated Omega: [[2.415e-05 2.521e-07 1.343e-07 1.330e-07 2.917e-07] [2.521e-07 5.465e-07 1.818e-07 4.615e-07 2.428e-07] [1.343e-07 1.818e-07 1.431e-07 1.687e-07 1.432e-07] [1.330e-07 4.615e-07 1.687e-07 4.396e-07 1.877e-07] [2.917e-07 2.428e-07 1.432e-07 1.877e-07 4.399e-07]]

(Correlation): [[1. 0.069 0.072 0.041 0.09 ] [0.069 1. 0.65 0.941 0.495] [0.072 0.65 1. 0.673 0.571] [0.041 0.941 0.673 1. 0.427] [0.09 0.495 0.571 0.427 1. ]]

Estimated Sigma: [[1.037 0.006 0.007 0.01 0.009] [0.006 1.009 0.148 0.428 0.06 ] [0.007 0.148 1.009 0.104 0.051] [0.01 0.428 0.104 1.011 0.022] [0.009 0.06 0.051 0.022 1.074]]

(Correlation): [[1. 0.006 0.006 0.01 0.008] [0.006 1. 0.147 0.424 0.057] [0.006 0.147 1. 0.103 0.049] [0.01 0.424 0.103 1. 0.021] [0.008 0.057 0.049 0.021 1. ]]

MTAG weight factors: (average across SNPs) [1.449 1.122 0.885 1.072 1.566] 2023/05/10/02:37:43 PM <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> 2023/05/10/02:37:43 PM grid point indices for max FDR for each trait: [ 6446 22109 49560 16399 49887] 2023/05/10/02:37:43 PM Maximum FDR 2023/05/10/02:37:43 PM Max FDR of Trait 1: 0.000719861182986 at probs = [0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.3 0.4 0.1 0. 0. 0.1 0. 0. 0. 0. 0. 0.1 0. 0. 0. 0. 0. ] 2023/05/10/02:37:43 PM Max FDR of Trait 2: 0.00026412815341 at probs = [0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.1 0. 0. 0.3 0.3 0. 0. 0. 0. 0. 0.2 0. 0. 0. 0. 0.1 0. 0. 0. 0. 0. ] 2023/05/10/02:37:43 PM Max FDR of Trait 3: 0.0470209444174 at probs = [0. 0. 0. 0. 0. 0.1 0. 0. 0. 0. 0. 0.1 0. 0. 0.3 0.3 0. 0. 0. 0. 0. 0.1 0. 0. 0. 0. 0. 0.1 0. 0. 0. 0. ] 2023/05/10/02:37:43 PM Max FDR of Trait 4: 0.0409180338017 at probs = [0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.4 0.4 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.1 0. 0. 0.1 0. 0. ] 2023/05/10/02:37:43 PM Max FDR of Trait 5: 0.0568193722102 at probs = [0. 0. 0. 0. 0. 0.1 0. 0. 0. 0. 0. 0.2 0. 0. 0.1 0.3 0. 0. 0. 0. 0. 0.1 0. 0. 0. 0. 0. 0. 0. 0. 0.2 0. ] 2023/05/10/02:37:43 PM <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> 2023/05/10/02:37:43 PM Completed FDR calculations. 2023/05/10/02:37:43 PM MTAG complete. Time elapsed: 4.0d:22.0h:19.0m:32.5189890862s

Looking forward to hearing from you.

Many thanks and best wishes,

Suzy

MTAG.log

[paturley]

Hi Suzy,

MaxFDR gives the potential maximum FDR for MTAG results. So a maxFDR means that up to 5% of the SNPs that are genome-wide significant may be false positives. Depending on your application, that may not be so bad. Mostly just just need to be sure to report it when you report your MTAG results.

Best, Patrick

On Tue, May 16, 2023 at 6:56 AM SuzyCC719 @.***> wrote:

Hi Patrick,

I have some issues when running MTAG. When I calculated maxFDR with 5 traits, the maxFDR for trait 5 was around 0.057. Could you please help me with interpreting these results? Is it suitable to use MTAG for these five traits?

The summary of MTAG results was listed below: Trait # SNPs used N (max) N (mean) GWAS mean chi^2 MTAG mean chi^2 GWAS equiv. (max) N 1 .../1_MTAG.txt 7169289 29006 21321 1.617 1.619 29104 2 ...2_MTAG.txt 7169289 1165720 1147707 1.625 1.662 1234512 3 ...3_MTAG.txt 7169289 964057 931789 1.132 1.319 2324005 4 ...4_MTAG.txt 7169289 471717 471717 1.205 1.571 1314393 5 ...5_MTAG.txt 7169289 278024 278024 1.114 1.229 557948

Estimated Omega: [[2.415e-05 2.521e-07 1.343e-07 1.330e-07 2.917e-07] [2.521e-07 5.465e-07 1.818e-07 4.615e-07 2.428e-07] [1.343e-07 1.818e-07 1.431e-07 1.687e-07 1.432e-07] [1.330e-07 4.615e-07 1.687e-07 4.396e-07 1.877e-07] [2.917e-07 2.428e-07 1.432e-07 1.877e-07 4.399e-07]]

(Correlation): [[1. 0.069 0.072 0.041 0.09 ] [0.069 1. 0.65 0.941 0.495] [0.072 0.65 1. 0.673 0.571] [0.041 0.941 0.673 1. 0.427] [0.09 0.495 0.571 0.427 1. ]]

Estimated Sigma: [[1.037 0.006 0.007 0.01 0.009] [0.006 1.009 0.148 0.428 0.06 ] [0.007 0.148 1.009 0.104 0.051] [0.01 0.428 0.104 1.011 0.022] [0.009 0.06 0.051 0.022 1.074]]

(Correlation): [[1. 0.006 0.006 0.01 0.008] [0.006 1. 0.147 0.424 0.057] [0.006 0.147 1. 0.103 0.049] [0.01 0.424 0.103 1. 0.021] [0.008 0.057 0.049 0.021 1. ]]

MTAG weight factors: (average across SNPs) [1.449 1.122 0.885 1.072 1.566] 2023/05/10/02:37:43 PM <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> 2023/05/10/02:37:43 PM grid point indices for max FDR for each trait: [ 6446 22109 49560 16399 49887] 2023/05/10/02:37:43 PM Maximum FDR 2023/05/10/02:37:43 PM Max FDR of Trait 1: 0.000719861182986 at probs = [0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.3 0.4 0.1 0. 0. 0.1 0. 0. 0. 0. 0. 0.1 0. 0. 0. 0. 0. ] 2023/05/10/02:37:43 PM Max FDR of Trait 2: 0.00026412815341 at probs = [0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.1 0. 0. 0.3 0.3 0. 0. 0. 0. 0. 0.2 0. 0. 0. 0. 0.1 0. 0. 0. 0. 0. ] 2023/05/10/02:37:43 PM Max FDR of Trait 3: 0.0470209444174 at probs = [0. 0. 0. 0. 0. 0.1 0. 0. 0. 0. 0. 0.1 0. 0. 0.3 0.3 0. 0. 0. 0. 0. 0.1 0. 0. 0. 0. 0. 0.1 0. 0. 0. 0. ] 2023/05/10/02:37:43 PM Max FDR of Trait 4: 0.0409180338017 at probs = [0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.4 0.4 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.1 0. 0. 0.1 0. 0. ] 2023/05/10/02:37:43 PM Max FDR of Trait 5: 0.0568193722102 at probs = [0. 0. 0. 0. 0. 0.1 0. 0. 0. 0. 0. 0.2 0. 0. 0.1 0.3 0. 0. 0. 0. 0. 0.1 0. 0. 0. 0. 0. 0. 0. 0. 0.2 0. ] 2023/05/10/02:37:43 PM <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> 2023/05/10/02:37:43 PM Completed FDR calculations. 2023/05/10/02:37:43 PM MTAG complete. Time elapsed: 4.0d:22.0h:19.0m:32.5189890862s

Looking forward to hearing from you.

Many thanks and best wishes,

Suzy

MTAG.log https://github.com/JonJala/mtag/files/11486262/MTAG.log

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