gskat_seq_cont: Perform GEE_KM Score Test with sequencing data for continuous...

In xfwang/gskat: GEE_KM

Description

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

Usage

gskat_seq_cont(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 or not
np	No. of perturbed samples

Value

p1	Returns asymptotic p-value
p2	Returns resampling p-value

Author(s)

Xuefeng Wang

Examples

		# gskat_seq_cont(y,XC=X,Z,ID)

xfwang/gskat documentation built on May 4, 2019, 1:05 p.m.