gskat_score_pert: Perform GEE_SKAT Score Test (perturbation)

In gskat: GEE_KM

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

Author(s)

Xuefeng Wang

Examples

		gskat_score_pert(gdata)

gskat documentation built on May 2, 2019, 5:51 a.m.