Functional Network Analysis


[Up] [Top]

Documentation for package ‘netresponse’ version 1.65.0

Help Pages

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'