calcScoreStats

Function that is applied in ICsingleSNP() to calculate a score statistic and p-value for each
column of an n*p genotype matrix.

Implements the Interval-Censored Sequence Kernel Association (ICSKAT) test for testing the association between interval-censored time-to-event outcomes and groups of single nucleotide polymorphisms (SNPs). Interval-censored time-to-event data occur when the event time is not known exactly but can be deduced to fall within a given interval. For example, some medical conditions like bone mineral density deficiency are generally only diagnosed at clinical visits. If a patient goes for clinical checkups yearly and is diagnosed at, say, age 30, then the onset of the deficiency is only known to fall between the date of their age 29 checkup and the date of the age 30 checkup. Interval-censored data include right- and left-censored data as special cases. This package also implements the interval-censored Burden test and the ICSKATO test, which is the optimal combination of the ICSKAT and Burden tests. Please see the vignette for a quickstart guide. The paper describing these methods is " Inference for Set-Based Effects in Genetic Association Studies with Interval-Censored Outcomes" by Sun R, Zhu L, Li Y, Yasui Y, & Robison L (Biometrics 2023, <doi:10.1111/biom.13636>).

Ryan Sun

ICSKAT

Interval-Censored Sequence Kernel Association Test

Liang Zhu

calcScoreStats function

<dl><dt>x</dt>
<dd>n*1 vector of genotypes.</dd>
<dt>UgTerm</dt>
<dd>n*1 vector multiplier for the score statistic.</dd>
<dt>ggTerm</dt>
<dd>n*1 vector multiplier for the Igg term of the variance.</dd>
<dt>gtTermCommon</dt>
<dd>n*p matrix multiplier for the common part of the Igt term of the variance.</dd>
<dt>gtHalfL</dt>
<dd>n*(nknots+1) matrix multiplier for one half of the unique part of the Igt term of the variance.</dd>
<dt>gtHalfR</dt>
<dd>n*(nknots+1) matrix multiplier for one half of the unique part of the Igt term of the variance.</dd>
<dt>solveItt</dt>
<dd>p*p inverse of the Itt matrix from ICSKAT_fit_null().</dd></dl>

Arguments

calcScoreStats.R — calcScoreStats

<dl>

<dt>x</dt>
<dd>n*1 vector of genotypes.</dd>


<dt>UgTerm</dt>
<dd>n*1 vector multiplier for the score statistic.</dd>


<dt>ggTerm</dt>
<dd>n*1 vector multiplier for the Igg term of the variance.</dd>


<dt>gtTermCommon</dt>
<dd>n*p matrix multiplier for the common part of the Igt term of the variance.</dd>


<dt>gtHalfL</dt>
<dd>n*(nknots+1) matrix multiplier for one half of the unique part of the Igt term of the variance.</dd>


<dt>gtHalfR</dt>
<dd>n*(nknots+1) matrix multiplier for one half of the unique part of the Igt term of the variance.</dd>


<dt>solveItt</dt>
<dd>p*p inverse of the Itt matrix from ICSKAT_fit_null().</dd>

</dl>

calcScoreStats: calcScoreStats.R

Description

Usage

Value

Arguments