calcScoreStats {ICSKAT}

calcScoreStats.R

Description

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

Usage

calcScoreStats(x, UgTerm, ggTerm, gtTermCommon, gtHalfL, gtHalfR, solveItt)

Arguments

x

n*1 vector of genotypes.

UgTerm

n*1 vector multiplier for the score statistic.

ggTerm

n*1 vector multiplier for the Igg term of the variance.

gtTermCommon

n*p matrix multiplier for the common part of the Igt term of the variance.

gtHalfL

n*(nknots+1) matrix multiplier for one half of the unique part of the Igt term of the variance.

gtHalfR

n*(nknots+1) matrix multiplier for one half of the unique part of the Igt term of the variance.

solveItt

p*p inverse of the Itt matrix from ICSKAT_fit_null().

Value

A 2*1 vector with the test statistic and then p-value.