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netresponse (version 1.32.2)

Functional Network Analysis

Description

Algorithms for functional network analysis. Includes an implementation of a variational Dirichlet process Gaussian mixture model for nonparametric mixture modeling.

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Version

Version

1.32.2

License

GPL (>=2)

Issues

1

Pull Requests

0

Stars

3

Forks

1

Maintainer

Leo Lahti

Last Published

February 15th, 2017

Functions in netresponse (1.32.2)

ICMg.get.comp.memberships

ICMg.get.comp.memberships
getqofz,NetResponseModel-method

Sample-to-response matrix of probabilities P(r|s).
plot_responses

plot_responses
P.rs.joint

Description: Joint probabiity density for mode and sample group Mainly for internal use; documentation will be provided later. Tools for calculating densities with Gaussian mixture models.
P.S

Description: Probabiity density for sample Mainly for internal use; documentation will be provided later. Tools for calculating densities with Gaussian mixture models.
bic.select.best.mode

Select best mode with BIC
filter.network

filter.network
factor.responses.minimal

Factor responses (minimal)
list.responses.continuous.single

Investigate association of a continuous variable and the modes
P.rs.joint.individual

Description: Joint probabiity density for mode and sample Mainly for internal use; documentation will be provided later. Tools for calculating densities with Gaussian mixture models.
list.responses.factor

List significant responses
bic.mixture.multivariate

Multivariate BIC mixture
plot_response

plot_response
P.s.r

Description: Probabiity density for sample given mode Mainly for internal use; documentation will be provided later. Tools for calculating densities with Gaussian mixture models.
PlotMixtureBivariate

PlotMixtureBivariate
enrichment.list.factor.minimal

enrichment.list.factor
list.significant.responses

Listing significant responses
update.model.pair

update.model.pair
check.matrix

check.matrix
generate.toydata

generate.toydata
netresponse-package

NetResponse: Global modeling of transcriptional responses in interaction networks
plot_expression

plot_expression
filter.netw

filter.netw
list.responses.factor.minimal

List factor responses (minimal)
order.responses

order.responses
write.netresponse.results

Write NetResponse results summary into a file.
plot_matrix

Visualize a matrix with one or two-way color scale.
toydata

toydata
bic.mixture

BIC mixture
PlotMixtureMultivariate.deprecated

PlotMixtureMultivariate.deprecated
response.enrichment

Enrichment for a specified sample group in the given response.
vdp.mixt

vdp.mixt
get.dat,NetResponseModel-method

Get subnetwork data
ICMg.links.sampler

ICMg.links.sampler
P.Sr

Description: Probabiity density for sample group given mode Mainly for internal use; documentation will be provided later. Tools for calculating densities with Gaussian mixture models.
PlotMixtureMultivariate

PlotMixtureMultivariate
P.r.s

Description: Probabiity of mode given a sample (a data vector) Mainly for internal use; documentation will be provided later. Tools for calculating densities with Gaussian mixture models.
factor.responses

Factor responses
independent.models

independent.models
model.stats

model.stats
plot_scale

plot_scale
remove.negative.edges

remove.negative.edges
PlotMixture

Plot mixtures
add.ellipse

Add ellipse to an existing plot
get.mis

get.mis
pick.model.parameters

pick.model.parameters
osmo

Osmoshock data set (PPI and expression)
plotPCA

plotPCA
P.s.individual

Description: Probabiity density for individual sample Mainly for internal use; documentation will be provided later. Tools for calculating densities with Gaussian mixture models.
PlotMixtureUnivariate

Plot univariate mixtures
list.responses.continuous.multi

Investigate association of a continuous variable and the modes
mixture.model

Mixture model
set.breaks

Set breaks
plot_data

Plot observed data.
bic.mixture.univariate

Univariate BIC mixture
continuous.responses

Continuous responses
enrichment.list.factor

enrichment.list.factor
listify.groupings

Convert grouping info into a list; each element corresponds to a group and lists samples in that group.
check.network

check.network
vectorize.groupings

Convert grouping info into a vector; each element corresponds to a group and lists samples in that group.
plot_subnet

plot_subnet
get.model.parameters

get.model.parameters
find.similar.features

Find similar features with a given subnetwork.
pick.model.pairs

Pick model pairs
sample2response

sample2response
read.sif

Reading network files
plot_associations

Association strength between category labels and responses.
detect.responses

detect.responses
ICMg.combined.sampler

ICMg.combined.sampler
NetResponseModel-class

Class "NetResponseModel"
P.rS

Description: Probabiity of mode given multiple samples (ie. data matrix) Mainly for internal use; documentation will be provided later. Tools for calculating densities with Gaussian mixture models.
centerData

Center data matrix.
dna

Dna damage data set (PPI and expression)
get.subnets,NetResponseModel-method

get.subnets
response2sample

response2sample