# Functional Network Analysis

## Documentation for package ‘netresponse’ version 1.18.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

netresponse-package | NetResponse: Global modeling of transcriptional responses in interaction networks
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)
enrichment.list.factor | Description: enrichment.list.factor
enrichment.list.factor.minimal | Description: enrichment.list.factor
factor.responses | Description: List responses for each level of the given factor
factor.responses.minimal | Description: List responses for each level of the given factor
find.similar.features | Find similar features with a given subnetwork.
get.dat | Get subnetwork data
get.dat-method | Get subnetwork data
get.model.parameters | get.model.parameters
get.subnets | get.subnets
get.subnets-method | get.subnets
ICMg.combined.sampler | ICMg.combined.sampler
ICMg.get.comp.memberships | ICMg.get.comp.memberships
ICMg.links.sampler | ICMg.links.sampler
list.responses.continuous.multi | Description: Investigate association of a continuous variable and the modes; given a list of groupings
list.responses.continuous.single | Description: Investigate association of a continuous variable and the modes
list.responses.factor | Description: List significantly associated responses for all factors and levels in the given annotation matrix
list.responses.factor.minimal | Description: List significantly associated responses for all factors and levels in the given annotation matrix
list.significant.responses | List responses with significant associations to a given sample group.
listify.groupings | Convert grouping info into a list; each element corresponds to a group and lists samples in that group.
mixture.model | Description: Fit Gaussian mixture model
model.stats | model.stats
netresponse | NetResponse: Global modeling of transcriptional responses in interaction networks
NetResponseModel-class | Class "NetResponseModel"
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
PlotMixture | PlotMixture
PlotMixtureBivariate | PlotMixtureBivariate
PlotMixtureMultivariate | PlotMixtureMultivariate
PlotMixtureMultivariate.deprecated | PlotMixtureMultivariate.deprecated
PlotMixtureUnivariate | PlotMixtureUnivariate
plotPCA | plotPCA
plot_associations | Association strength between category labels and responses.
plot_matrix | Visualize a matrix with one or two-way color scale. TODO: one-way color scale
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
show-method | Class "NetResponseModel"
toydata | toydata
vdp.mixt | vdp.mixt
vectorize.groupings | Convert grouping info into a vector; each element corresponds to a group and lists samples in that group.
write.netresponse.results | Write NetResponse results summary into a file.
[[-method | Class "NetResponseModel"