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==== Comparative runtimes for Firth and score tests. ====
==== Comparative runtimes for Firth and score tests. ====
Firth test is relatively computationally intensive compared to the score test. However, Firth has better test properties (i.e. type I error rates and power) compare to score test when analyzing low frequency variants in studies with unequal numbers of cases and controls.
Firth test is relatively computationally intensive compared to the score test. However, Firth has better test properties (i.e. type I error rates and power) compare to score test when analyzing low frequency variants in studies with unequal numbers of cases and controls.
For example, using 1 CPU, analyzing 2333 FUSION individuals, chromosome 20, 22755 SNPs (adjusting for age, sex and 11 dummy variables for birth province):
For example, using 1 CPU, analyzing 2333 FUSION individuals, chromosome 20, 22755 SNPs (adjusting for age, sex and 11 dummy variables for birth province):
*Firth test: 56 minutes
*Firth test: 56 minutes (3360 seconds)
*Score test: 32 seconds
*Score test: 32 seconds
<br> This is the reason why we only ask for Firth test results for SNPs with MAC <= 200.
This is the reason why we only ask for Firth test results for SNPs with MAC <= 200.
=== 1. Typical DIAGRAM analysis using existing association pipeline<br> ===
=== 1. Typical DIAGRAM analysis using existing association pipeline<br> ===
