# Functional Network Analysis

## Documentation for package ‘netresponse’ version 1.60.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- 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 | BIC mixture
bic.mixture.multivariate | Multivariate BIC mixture
bic.mixture.univariate | Univariate BIC mixture
bic.select.best.mode | Select best mode with BIC
centerData | Center data matrix.
check.network | check.network
continuous.responses | Continuous responses
detect.responses | detect.responses
dna | Dna damage data set (PPI and expression)
enrichment.list.factor | enrichment.list.factor
enrichment.list.factor.minimal | enrichment.list.factor
factor.responses | Factor responses
factor.responses.minimal | Factor responses (minimal)
find.similar.features | Find similar features with a given subnetwork.
get.dat | Get subnetwork data
get.dat-method | Get subnetwork data
get.mis | get.mis
get.model.parameters | get.model.parameters
get.subnets | get.subnets
get.subnets-method | get.subnets
list.responses.continuous.multi | Investigate association of a continuous variable and the modes
list.responses.continuous.single | Investigate association of a continuous variable and the modes
list.responses.factor | List significant responses
list.responses.factor.minimal | List factor responses (minimal)
list.significant.responses | Listing significant responses
listify.groupings | Convert grouping info into a list; each element corresponds to a group and lists samples in that group.
mixture.model | 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)
PlotMixture | Plot mixtures
PlotMixtureBivariate | PlotMixtureBivariate
PlotMixtureMultivariate | PlotMixtureMultivariate
PlotMixtureUnivariate | Plot univariate mixtures
plotPCA | plotPCA
plot_associations | Association strength between category labels and responses.
plot_data | Plot observed data.
plot_expression | plot_expression
plot_matrix | Visualize a matrix with one or two-way color scale.
plot_response | plot_response
plot_responses | plot_responses
plot_scale | plot_scale
plot_subnet | plot_subnet
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'
split.qofz | split.qofz
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'