NetResponse: functional network analysis


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Documentation for package ‘netresponse’ version 1.12.0

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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
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.dat-method Class "NetResponseModel"
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 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 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
plotAssociations Association strength between category labels and responses.
PlotMixture PlotMixture
PlotMixtureBivariate PlotMixtureBivariate
PlotMixtureMultivariate PlotMixtureMultivariate
PlotMixtureMultivariate.deprecated PlotMixtureMultivariate.deprecated
PlotMixtureUnivariate PlotMixtureUnivariate
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
show-method Class "NetResponseModel"
toydata toydata
vdp.mixt vdp.mixt
write.netresponse.results Write NetResponse results summary into a file.
[[-method Class "NetResponseModel"