Description Details Author(s) References See Also Examples
The package includes functions for fitting hierarchical semiparametric regression model to a large number of parametric test statistics
Package: | hisemi |
Type: | Package |
Version: | 1.1-0 |
Date: | 2017-07-09 |
License: | GPL version 2 or newer |
LazyLoad: | yes |
penLik.EMNewton
is the major interface function to be called.
coef.hisemit
extracts the estimated parameters.
confint.hisemit
returns the confidence intervals.
directSum
computes the direct sum of matrices.
EMupdate
is the EM algorithm used in penLik.EMNewton
.
fitted.hisemit
extracts the fitted values.
logLik.hisemit
returns the log likelihood.
NRupdate
is the Newton-Raphson algorithm used in penLik.EMNewton
.
plot.hisemit
plots the fitted model.
print.hisemit
print summary information.
residuals.hisemit
returns the residuals.
scaledTMix.null
fits the null model with common pi0.
scaledTMix.psat
fits the partially saturated model with free pi0 and common scale factor.
scaledTMix.sat
fits the completely saturated model with free pi0 and free scale factor.
vcov.hisemit
returns the sandwich variance-covariance matrix.
Long Qu rtistician@gmail.com
Maintainer: Long Qu rtistician@gmail.com
Long Qu, Dan Nettleton, Jack Dekkers (2012). A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics, 68(4):1168-1177
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | ## simulate some fake data
G=100 ## for demonstration only. Normally, G should be much larger
sdncp=1.3
n1=n2=5
df=n1+n2-2
set.seed(54457704)
x=runif(G,1,G)
f=function(x)sin(x*pi/1000)+1
Pi.i=1/(1+exp(f(x)))
Z.i=rbinom(G,1,1-Pi.i)
t0.i=rt(G,df)
ncp.i=rnorm(G,0,sdncp)
t1.i=rt(G,df, ncp.i)
t.i=ifelse(Z.i==0,t0.i,t1.i)
## fit model
(plfit=penLik.EMNewton(t.i, x, df, spar=10^seq(0,8,length=30),plotit=FALSE))
(plfit0=scaledTMix.null(t.i, df))
## Not run:
plot(plfit)
plot(t.i, plfit$lfdr, pch='.')
lines(sort(t.i), plfit0$lfdr[order(t.i)], col=2, lwd=3)
## End(Not run)
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