STE: Score test with the most probable CNV

In PedCNV: An implementation for association analysis with CNV data.

Description

Calculates the score test statistics with the most probable CNV.

Usage

  STE(envirX, clusRes, fam, alpha, phi, sig2g, sig2)

Arguments

envirX	The matrix of environmental variables. The intercept should be included if it's needed.
fam	The FAM file which follows the format defined in PLINK.
clusRes	The clustering group which is signed to each individual.
alpha	The estimated parameters for environmental variables under null hypothesis. This value can be calculated by using function AssoTestProc.
phi	The matrix of correlation between individuals.
sig2g	The estimated standard error for polygenic effect under null hypothesis. This value can be calculated by using function AssoTestProc.
sig2	The estimated standard error for environmental effect under null hypothesis. This value can be calculated by using function AssoTestProc.

Value

It returns the statistic value and pvalue of the score test.

STEs	The statistic value of score test with the most probable CNV.
STEp	The pvalue of score test with the most probable CNV.

Author(s)

Meiling Liu, Sungho Won

Examples

# Fit the data under the assumption that there are 3 clusters
asso.fit <- AssoTestProc(signal=signal,fam=fam,envirX=envirX,phi=phi,N=3,varSelection='PC.9')
cnv_e <- asso.fit$clusRes
alpha <- asso.fit$para$alpha
sig2g <- asso.fit$para$sig2g
sig2 <- asso.fit$para$sig2
STE(envirX=envirX,clusRes=cnv_e,fam=fam,alpha=alpha,phi=phi,sig2g=sig2g,sig2=sig2)

PedCNV documentation built on May 2, 2019, 8:17 a.m.