gskat (version 1.0)

gskat_score_pert: Perform GEE_SKAT Score Test (perturbation)

Description

This function performs family based marker set based association (score test) based on the GEE_SKAT.

Usage

gskat_score_pert(pedDat,F1=FALSE,pw="Rade",np=10000)

Arguments

pedDat

Input Family Data: A list including four data matrix: ID, y, X, Z. ID: Pedigree ID matrix. The four columns are the Family ID (FID), Individual ID (IID), Paternal ID (FAT), Maternal ID (MAT), respectively. y: binary phenotype coded as 0, 1 X: covaraite matrix, including the intercept column Z: SNP genotypes coded 0/1/2 (minor allele count).

F1

If TRUE, use identity working corr. matrix

pw

Perturbation method."Rade":Rademacher; "Norm": Normal distribution

np

number of perturbed samples. default=10000

Value

pval

Returns p-value

Ts

Score statistic

mu_Ts

Theoretical mean of Ts

var_Ts

Theoretical variance of Ts

PM

Empirical mean of Ts based on the perturbation

PV

Empirical variance of Ts based on the perturbation

Examples

		gskat_score_pert(gdata)