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' |