Man pages for netresponse
Functional Network Analysis

add.ellipseAdd ellipse to an existing plot
bic.mixtureBIC mixture
bic.mixture.multivariateMultivariate BIC mixture
bic.mixture.univariateUnivariate BIC mixture
bic.select.best.modeSelect best mode with BIC
centerDataCenter data matrix.
check.matrixcheck.matrix
check.networkcheck.network
continuous.responsesContinuous responses
detect.responsesdetect.responses
dnaDna damage data set (PPI and expression)
enrichment.list.factorenrichment.list.factor
enrichment.list.factor.minimalenrichment.list.factor
factor.responsesFactor responses
factor.responses.minimalFactor responses (minimal)
filter.netwfilter.netw
filter.networkfilter.network
find.similar.featuresFind similar features with a given subnetwork.
generate.toydatagenerate.toydata
get.dat-NetResponseModel-methodGet subnetwork data
get.misget.mis
get.model.parametersget.model.parameters
getqofz-NetResponseModel-methodSample-to-response matrix of probabilities P(r|s).
get.subnets-NetResponseModel-methodget.subnets
ICMg.combined.samplerICMg.combined.sampler
ICMg.get.comp.membershipsICMg.get.comp.memberships
ICMg.links.samplerICMg.links.sampler
independent.modelsindependent.models
listify.groupingsConvert grouping info into a list; each element corresponds...
list.responses.continuous.multiInvestigate association of a continuous variable and the...
list.responses.continuous.singleInvestigate association of a continuous variable and the...
list.responses.factorList significant responses
list.responses.factor.minimalList factor responses (minimal)
list.significant.responsesListing significant responses
mixture.modelMixture model
model.statsmodel.stats
NetResponseModel-classClass "NetResponseModel"
netresponse-packageNetResponse: Global modeling of transcriptional responses in...
order.responsesorder.responses
osmoOsmoshock data set (PPI and expression)
pick.model.pairsPick model pairs
pick.model.parameterspick.model.parameters
plot_associationsAssociation strength between category labels and responses.
plot_dataPlot observed data.
plot_expressionplot_expression
plot_matrixVisualize a matrix with one or two-way color scale.
PlotMixturePlot mixtures
PlotMixtureBivariatePlotMixtureBivariate
PlotMixtureMultivariatePlotMixtureMultivariate
PlotMixtureMultivariate.deprecatedPlotMixtureMultivariate.deprecated
PlotMixtureUnivariatePlot univariate mixtures
plotPCAplotPCA
plot_responseplot_response
plot_responsesplot_responses
plot_scaleplot_scale
plot_subnetplot_subnet
P.r.sDescription: Probabiity of mode given a sample (a data...
P.rSDescription: Probabiity of mode given multiple samples (ie....
P.rs.jointDescription: Joint probabiity density for mode and sample...
P.rs.joint.individualDescription: Joint probabiity density for mode and sample...
P.SDescription: Probabiity density for sample Mainly for...
P.s.individualDescription: Probabiity density for individual sample Mainly...
P.s.rDescription: Probabiity density for sample given mode Mainly...
P.SrDescription: Probabiity density for sample group given mode...
read.sifReading network files
remove.negative.edgesremove.negative.edges
response2sampleresponse2sample
response.enrichmentEnrichment for a specified sample group in the given...
sample2responsesample2response
set.breaksSet breaks
toydatatoydata
update.model.pairupdate.model.pair
vdp.mixtvdp.mixt
vectorize.groupingsConvert grouping info into a vector; each element corresponds...
write.netresponse.resultsWrite NetResponse results summary into a file.
netresponse documentation built on Nov. 1, 2018, 2:59 a.m.