ICMg.combined.sampler   ICMg.combined.sampler
ICMg.get.comp.memberships
                        ICMg.get.comp.memberships
ICMg.links.sampler      ICMg.links.sampler
NetResponseModel-class
                        Class "NetResponseModel"
PlotMixtureBivariate    PlotMixtureBivariate
PlotMixtureMultivariate
                        PlotMixtureMultivariate
add.ellipse             Add ellipse to an existing plot.
bic.mixture             Description: Latent class analysis based on
                        (infinite) Gaussian mixture model. If the input
                        is data matrix, a multivariate model is fitted;
                        if the input is a vector, a univariate model is
                        fitted
bic.mixture.multivariate
                        Description: Latent class analysis based on
                        (infinite) Gaussian mixture model. If the input
                        (dat) is data matrix, a multivariate model is
                        fitted.
bic.mixture.univariate
                        Description: Latent class analysis based on
                        (infinite) Gaussian mixture model. If the input
                        (dat) is data matrix, a multivariate model is
                        fitted. If the input is a vector or a
                        1-dimensional matrix, a univariate model is
                        fitted.
bic.select.best.mode    Description: Select optimal number of mixture
                        components by adding components until the
                        increase in objective function is below
                        threshold.
centerData              Center data matrix.
continuous.responses    Description: Quantify association between modes
                        and continuous variable
detect.responses        detect.responses
dna                     Dna damage data set (PPI and expression)
factor.responses        Description: List responses for each level of
                        the given factor
find.similar.features   Find similar features with a given subnetwork.
get.dat                 get.dat
get.model.parameters    get.model.parameters
get.subnets             get.subnets
list.responses.continuous
                        Description: Investigate association of a
                        continuous variable and the modes
list.responses.factor   Description: List responses for all factors and
                        levels in the given annotation matrix
list.significant.responses
                        List responses with significant associations to
                        a given sample group.
mixture.model           Description: Fit Gaussian mixture model
model.stats             model.stats
netresponse-package     NetResponse: Global modeling of transcriptional
                        responses in interaction networks
order.responses         order.responses
osmo                    Osmoshock data set (PPI and expression)
plot.data               Plot observed data.
plot.expression         plot.expression
plot.response           plot.response
plot.responses          plot.responses
plot.scale              plot.scale
plot.subnet             plot.subnet
plotAssociations        Association strength between category labels
                        and responses.
plotPCA                 plotPCA
read.sif                Reading network files
response.enrichment     Enrichment for a specified sample group in the
                        given response.
response2sample         response2sample
sample2response         sample2response
set.breaks              set.breaks
toydata                 toydata
vdp.mixt                vdp.mixt
write.netresponse.results
                        Write NetResponse results summary into a file.
