mtag
mtag copied to clipboard
JonJala
maxFDR calculation has no results with ending
Dear authors, Thank you for this software. I used the MTAG without errors. But when I checked the log file, I found that there was no maxFDR results when I used 5 traits to calculate it, but 3 traits worked well. The end of log file is here:
(Correlation): [[ 1. 0.171 0.172 0.73 0.337] [ 0.171 1. 0.336 0.242 0.439] [ 0.172 0.336 1. 0.15 0.527] [ 0.73 0.242 0.15 1. 0.374] [ 0.337 0.439 0.527 0.374 1. ]]
Estimated Sigma: [[ 1.067 0.014 0.037 0.278 0.085] [ 0.014 1.008 0.36 0.011 0.149] [ 0.037 0.36 1.037 0.032 0.178] [ 0.278 0.011 0.032 1.126 0.07 ] [ 0.085 0.149 0.178 0.07 0.999]]
(Correlation): [[ 1. 0.014 0.035 0.254 0.083] [ 0.014 1. 0.353 0.01 0.148] [ 0.035 0.353 1. 0.03 0.175] [ 0.254 0.01 0.03 1. 0.066] [ 0.083 0.148 0.175 0.066 1. ]]
MTAG weight factors: (average across SNPs) [ 1.229 1.455 1.376 1.256 1.087]
2020/07/08/09:31:56 PM
2020/07/08/09:31:56 PM MTAG results saved to file.
2020/07/08/09:31:56 PM Beginning maxFDR calculations. Depending on the number of grid points specified, this might take some time...
2020/07/08/09:31:56 PM T=5
Hello,
I presume that it is just taking too long to converge with so many phenotypes. As it says in the MTAG paper "Since p has 2^T elements, [maxFDR] may be computationally infeasible to perform a fine grid search when T is larger than three or four traits." You may consider calculating the maxFDR with a subset of the phenotypes, in particular if some of the phenotypes in the subset have substantially larger mean chi2 stats or lower genetic correlations.
On Wed, Jul 8, 2020 at 8:20 PM whecrane [email protected] wrote:
Dear authors, Thank you for this software. I used the MTAG without errors. But when I checked the log file, I found that there was no maxFDR results when I used 5 traits to calculate it, but 3 traits worked well. The end of log file is here:
(Correlation): [[ 1. 0.171 0.172 0.73 0.337] [ 0.171 1. 0.336 0.242 0.439] [ 0.172 0.336 1. 0.15 0.527] [ 0.73 0.242 0.15 1. 0.374] [ 0.337 0.439 0.527 0.374 1. ]]
Estimated Sigma: [[ 1.067 0.014 0.037 0.278 0.085] [ 0.014 1.008 0.36 0.011 0.149] [ 0.037 0.36 1.037 0.032 0.178] [ 0.278 0.011 0.032 1.126 0.07 ] [ 0.085 0.149 0.178 0.07 0.999]]
(Correlation): [[ 1. 0.014 0.035 0.254 0.083] [ 0.014 1. 0.353 0.01 0.148] [ 0.035 0.353 1. 0.03 0.175] [ 0.254 0.01 0.03 1. 0.066] [ 0.083 0.148 0.175 0.066 1. ]]
MTAG weight factors: (average across SNPs) [ 1.229 1.455 1.376 1.256 1.087]
2020/07/08/09:31:56 PM 2020/07/08/09:31:56 PM MTAG results saved to file. 2020/07/08/09:31:56 PM Beginning maxFDR calculations. Depending on the number of grid points specified, this might take some time... 2020/07/08/09:31:56 PM T=5
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/JonJala/mtag/issues/99, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFBUB5I4LHX7UOQ5VKESPQTR2UENRANCNFSM4OVCHZBQ .
