Nothing
## ---- message=FALSE, warning=FALSE--------------------------------------------
library(graper)
library(ggplot2)
## -----------------------------------------------------------------------------
set.seed(123)
data <- makeExampleData(n=200, p=320, g=4,
pis=c(0.05, 0.1, 0.05, 0.1),
gammas=c(0.1, 0.1, 10, 10),
response="bernoulli")
# training data set
Xtrain <- data$X[1:100, ]
ytrain <- data$y[1:100]
# annotations of features to groups
annot <- data$annot
# test data set
Xtest <- data$X[101:200, ]
ytest <- data$y[101:200]
## -----------------------------------------------------------------------------
fit <- graper(Xtrain, ytrain, annot, verbose=FALSE,
family="binomial", calcELB=FALSE)
fit
## -----------------------------------------------------------------------------
plotPosterior(fit, "gamma", gamma0=data$gammas)
plotPosterior(fit, "pi", pi0=data$pis)
## -----------------------------------------------------------------------------
# get coefficients (without the intercept)
beta <- coef(fit, include_intercept=FALSE)
# beta <- fit$EW_beta
# plot estimated versus true beta
qplot(beta, data$beta)
## -----------------------------------------------------------------------------
# get intercept
intercept <- fit$intercept
## -----------------------------------------------------------------------------
# get estimated posterior inclusion probabilities per feature
pips <- getPIPs(fit)
## -----------------------------------------------------------------------------
preds <- predict(fit, Xtest)
## -----------------------------------------------------------------------------
sessionInfo()
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