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


Rind

0.054

<a onClick="popup('http://www.biomedcentral.com/1471-2156/13/7/mathml/M70','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/13/7/mathml/M70">View MathML</a>

0.051

BSSU

0.053

BaSSUOrd

0.06


Rsum

0.053

<a onClick="popup('http://www.biomedcentral.com/1471-2156/13/7/mathml/M71','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/13/7/mathml/M71">View MathML</a>

0.054

BSSUw

0.042

BaSSUwOrd

0.062


Cbon

0.054

Bind

0.055

BaSSU

0.062

BwSC

0.042


Clogit

0.055

Bsum

0.058

BaSSUw

0.055

BwSCd

0.051


BwSum

0.055

BwOR

0.062

BKML

0.056


There is customized LD structure among common variants and among rare variants. Rind, collapsing method by indicator function on rare variants. Rsum, collapsing method by sum function on rare variants. <a onClick="popup('http://www.biomedcentral.com/1471-2156/13/7/mathml/M72','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/13/7/mathml/M72">View MathML</a>, selective Rind. <a onClick="popup('http://www.biomedcentral.com/1471-2156/13/7/mathml/M73','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2156/13/7/mathml/M73">View MathML</a> selective Rsum . Cbon, single test with bonferroni correction on common variants. Clogit, multivariate logistic regression test on common variants. Bind and Bsum, Clogit with collapsed component from rare variants. BwSum, weighted sum test. BwOR Odds Ratio based weighted sum test. BSSU, BSSUw , SSU based tests. BaSSU, BaSSUw, adaptive sum tests. BaSSUOrd, BaSSUwOrd ordered adaptive sum tests. BKML, Logistic Kernel-Machine Test. BwSC, BwSCd selectively weighted collapsing.

Dai et al. BMC Genetics 2012 13:7   doi:10.1186/1471-2156-13-7

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