Man pages for netresponse
Functional Network Analysis
| 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.matrix | check.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) |
| filter.netw | filter.netw |
| filter.network | filter.network |
| find.similar.features | Find similar features with a given subnetwork. |
| generate.toydata | generate.toydata |
| get.dat-NetResponseModel-method | Get subnetwork data |
| get.mis | get.mis |
| get.model.parameters | get.model.parameters |
| getqofz-NetResponseModel-method | Sample-to-response matrix of probabilities P(r|s). |
| get.subnets-NetResponseModel-method | get.subnets |
| independent.models | independent.models |
| listify.groupings | Convert grouping info into a list; each element corresponds... |
| list.responses.continuous.multi | Investigate association of a continuous variable and the... |
| list.responses.continuous.single | Investigate association of a continuous variable and the... |
| list.responses.factor | List significant responses |
| list.responses.factor.minimal | List factor responses (minimal) |
| list.significant.responses | Listing significant responses |
| mixture.model | Mixture model |
| model.stats | model.stats |
| NetResponseModel-class | Class 'NetResponseModel' |
| netresponse-package | NetResponse: Global modeling of transcriptional responses in... |
| order.responses | order.responses |
| osmo | Osmoshock data set (PPI and expression) |
| pick.model.pairs | Pick model pairs |
| pick.model.parameters | pick.model.parameters |
| 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. |
| PlotMixture | Plot mixtures |
| PlotMixtureBivariate | PlotMixtureBivariate |
| PlotMixtureMultivariate | PlotMixtureMultivariate |
| PlotMixtureUnivariate | Plot univariate mixtures |
| plotPCA | plotPCA |
| plot_response | plot_response |
| plot_responses | plot_responses |
| plot_scale | plot_scale |
| plot_subnet | plot_subnet |
| P.r.s | Description: Probabiity of mode given a sample (a data... |
| P.rS | Description: Probabiity of mode given multiple samples (ie.... |
| P.rs.joint | Description: Joint probabiity density for mode and sample... |
| P.rs.joint.individual | Description: Joint probabiity density for mode and sample... |
| P.S | Description: Probabiity density for sample Mainly for... |
| P.s.individual | Description: Probabiity density for individual sample Mainly... |
| P.s.r | Description: Probabiity density for sample given mode Mainly... |
| P.Sr | Description: Probabiity density for sample group given mode... |
| read.sif | Reading network files |
| remove.negative.edges | remove.negative.edges |
| response2sample | response2sample |
| response.enrichment | Enrichment for a specified sample group in the given... |
| sample2response | sample2response |
| set.breaks | Set breaks |
| split.qofz | split.qofz |
| toydata | toydata |
| update.model.pair | update.model.pair |
| vdp.mixt | vdp.mixt |
| vectorize.groupings | Convert grouping info into a vector; each element corresponds... |
| write.netresponse.results | Write NetResponse results summary into a file. |
