gskat (version 1.0)

gskat_seq: Perform GEE_KM Score Test with sequencing data

Description

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

Usage

gskat_seq(y,XC,Z,ID,impute.method="fixed",SNP.weights=NULL,
	w_a=1,w_b=25,resampling=TRUE,pw="Rade",Uc=TRUE,sW=FALSE,np=10000)

Arguments

y

binary phenotype coded as 0, 1

XC

covaraite matrix, including the intercept column

Z

SNP genotypes coded 0/1/2 (minor allele count)

ID

ID: Pedigree ID matrix, having four columns are the Family ID (FID), Individual ID (IID), Paternal ID (FAT), Maternal ID (MAT), respectively.

impute.method

default is fixed method i.e. fill with means

SNP.weights

If NULL, the default beta (1,25) desensity will be used, or a custimoized weight vector may be used

w_a

The first parameter of the beta density in the weight function

w_b

The second parameter of the beta density in the weight function

resampling

If TRUE, resampling will be applied

pw

r.v. used in the perturbation, "Norm"=Normal , "Rade"=Rademacher

Uc

Score centered or not

sW

standardize weights

np

No. of perturbed samples

Value

p1

Returns asymptotic p-value

p2

Returns resampling p-value

Examples

		# gskat_score(gdata)$p2