Hi everyone,
I am doing the PRS with PRSice, I set as follow
...
--lower 0 \
--interval 0.01 \
--upper 0.85 \
...
the result in the .prsice is as follow
Set Threshold R2 P Coefficient Standard.Error Num_SNP
Base 0.11 0.0573236 2.14869e-05 1.41723 0.323538 1
Base 0.16 0.0820505 2.23083e-07 2.28802 0.42246 2
Base 0.23 0.124923 3.67078e-11 3.3304 0.468058 3
Base 0.44 0.212734 5.69775e-21 6.80455 0.624526 10
Base 0.46 0.225492 1.00129e-22 7.28094 0.631047 12
Base 0.57 0.223171 2.12793e-22 7.39902 0.647995 13
Base 0.6 0.238986 1.0476e-24 8.42251 0.68701 21
Base 0.62 0.244352 1.56133e-25 9.09485 0.724074 27
Base 0.7 0.251666 1.06589e-26 9.4993 0.731542 31
Base 0.76 0.2574 1.20287e-27 10.3398 0.775632 44
Base 0.77 0.265801 4.31103e-29 12.4527 0.898506 116
Base 0.78 0.265607 4.6651e-29 12.4531 0.899346 117
Base 0.79 0.26775 1.9452e-29 12.616 0.902045 122
Base 0.81 0.268386 1.49709e-29 12.6483 0.901663 123
Base 0.82 0.268006 1.75044e-29 12.659 0.904032 124
Base 0.83 0.266628 3.07871e-29 12.6872 0.911902 131
Base 0.84 0.269101 1.11373e-29 12.9602 0.920808 146
Base 0.85 0.274744 1.0325e-30 13.4441 0.9301 171
Base 1 0.292076 3.96269e-34 118.58 7.54246 110070
I wonder why even though I have set the parameters as above the threshold jump is not as expected 0 - 0.01 - 0.02 - ... - 0.85. Does any know what happens with it?
Your help is really appreciated!
•
written
by
landscape95
1 answer
That is because we tried to optimize the speed of PRSice by ignoring thresholds that did not add any additional SNPs from previous thresholds.
For example, if my SNPs are SNP P-value SNP1 0.04 SNP2 0.045 SNP3 0.1 SNP4 0.2
Then with your threshold selection (0 - 0.85, step size of 0.01), we will only generate results for threshold
0.04, 0.05, 0.1 and 0.2, ignoring all thresholds in-between. You can savely duplicate the results for those other threshold if you want (e.g. results for threshold 0.05 to 0.09 should be identical as no new SNPs are added)
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