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A. DIAGRAMv4_iSNPs_XXX_1000G_KKK_FBC_YYY_ZZZ.epacts.gz
A. DIAGRAMv4_iSNPs_XXX_1000G_KKK_FBC_YYY_ZZZ.epacts.gz
B. DIAGRAMv4_iSNPs_XXX_adjBMI_1000G_KKK_FBC_YYY_ZZZ.epacts.gz
B. DIAGRAMv4_iSNPs_XXX_adjBMI_1000G_KKK_FBC_YYY_ZZZ.epacts.gz
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=== Analysis for QC ===
=== Analysis for QC ===
'''YYY '''indicates the DATE of file generation (MMDDYY format, e.g. 021710 – apologies in advance to our European colleagues)<br>'''ZZZ '''indicates the name + other initials of the uploader (e.g., BFV, LJS, ABC, etc.)
'''YYY '''indicates the DATE of file generation (MMDDYY format, e.g. 021710 – apologies in advance to our European colleagues)<br>'''ZZZ '''indicates the name + other initials of the uploader (e.g., BFV, LJS, ABC, etc.)
==== 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.
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
*Score test: 32 seconds
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> ===
