PedCNV (version 0.1)

STIM: Score test with the intensity value

Description

Calculates the score test statistics with the intensity value.

Usage

STIM(envirX, signal, 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.

signal

The matrix of intensity measurements. The row names must be consistent with the Individual ID in fam file.

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.

STIMs

The statistic value of score test with the intensity value under null hypothesis.

STIMp

The pvalue of score test with the intensity value under null hypothesis.

df

The degree of freedom of score test with the intenstiy value under null hypothesis.

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')
alpha <- asso.fit$para$alpha
sig2g <- asso.fit$para$sig2g
sig2 <- asso.fit$para$sig2
STIM(envirX=envirX,signal=signal,fam=fam,alpha=alpha,phi=phi,sig2g=sig2g,sig2=sig2)