Question: PRSice threshold result is not as expected
1
gravatar for landscape95
20 days ago by
landscape95160
landscape95160 wrote:

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!

gwas prsice • 82 views
ADD COMMENTlink modified 8 days ago by zx87546.5k • written 20 days ago by landscape95160
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