Weighted selective collapsing strategy for detecting rare and common variants in genetic association study

BMC Genomic Data

Table 1 Type I error rates for all tests in simulated data of scenario A

Test	Type-1 error	Test	Type-1 error	Test	Type-1 error	Test	Type-1 error
R _ind	0.054	$R_{i n d}^{S C}$	0.051	B _SSU	0.053	B _aSSUOrd	0.06
R _sum	0.053	$R_{s u m}^{S C}$	0.054	B _SSUw	0.042	B _aSSUwOrd	0.062
C _bon	0.054	B _ind	0.055	B _aSSU	0.062	B _wSC	0.042
C _logit	0.055	B _sum	0.058	B _aSSUw	0.055	B _wSCd	0.051
B _wSum	0.055	B _wOR	0.062	B _KML	0.056

There is customized LD structure among common variants and among rare variants. R_ind, collapsing method by indicator function on rare variants. R_sum, collapsing method by sum function on rare variants. $R_{i n d}^{S C}$ , selective R_ind. $R_{s u m}^{S C}$ selective R_sum . C_bon, single test with bonferroni correction on common variants. C_logit, multivariate logistic regression test on common variants. B_ind and B_sum, C_logit with collapsed component from rare variants. B_wSum, weighted sum test. B_wOR Odds Ratio based weighted sum test. B_SSU, B_SSUw , SSU based tests. B_aSSU, B_aSSUw, adaptive sum tests. B_aSSUOrd, B_aSSUwOrd ordered adaptive sum tests. B_KML, Logistic Kernel-Machine Test. B_wSC, B_wSCd selectively weighted collapsing.

ISSN: 2730-6844