gskat (version 1.0)

score_FSKAT_IC_pertu: GEE_SKAT for rare variants

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

See Also

score.RFAM_IC_burden

Examples

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