score_FSKAT_IC_pertu: GEE_SKAT for rare variants

In gskat: GEE_KM

Description

This function performs GEE_SKAT score test based on the davies and perturbation method

Usage

score_FSKAT_IC_pertu(y,XC,Z,ID,w_a=1,w_b=5,pw="Rade",Uc=FALSE,sW=TRUE,np=10000)

Arguments

y	binary phenotype coded as 0, 1
XC	covaraite matrix, WITHOUT the intercept column.
Z	SNP genotypes coded 0/1/2 (minor allele count).
ID	Pedigree ID matrix. The four columns are the Family ID (FID), Individual ID (IID), Paternal ID (FAT), Maternal ID (MAT), respectively.
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
pw	perturbatio method: "Rade"=Rademacher; "Norm"=Normal
Uc	Score centered or not
sW	standardize weights or not
np	No. of perturbed samples

Value

pval_davies	Returns p-value from davies method
ifault	fault indicator from the davies method: 0: no error, 1: requested accuracy could not be obtained, 2: round-off error possibly significant, 3: invalid parameters, 4: unable to locate integration parameters
PM	Empirical mean of Ts based on perturbation
mu_Ts	Theoretical mean of Ts
PV	Empirical variance of Ts based on perturbation
var_Ts	Theoretical variance of Ts
pval_pert	Returns p-value from perturbation method

Author(s)

Xuefeng Wang

See Also

score.RFAM_IC_burden

Examples

	score_FSKAT_IC_pertu(y=gdata$y,XC=gdata$X[,-1],Z=gdata$Z,ID=gdata$ID)

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