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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 |
| 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" |