Description Usage Arguments Value Author(s) Examples
Calculates the score test statistics with the intensity value.
1 |
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 |
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 |
sig2 |
The estimated standard error for
environmental effect under null hypothesis. This value
can be calculated by using function
|
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. |
Meiling Liu, Sungho Won
1 2 3 4 5 6 | # 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)
|
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