netresponse: Functional Network Analysis
Version 1.36.0

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

Browse man pages Browse package API and functions Browse package files

AuthorLeo Lahti, Olli-Pekka Huovilainen, Antonio Gusmao and Juuso Parkkinen
Bioconductor views CellBiology Clustering DifferentialExpression GeneExpression Genetics GraphAndNetwork Microarray Network Transcription
Date of publicationNone
MaintainerLeo Lahti <leo.lahti@iki.fi>
LicenseGPL (>=2)
Version1.36.0
URL https://github.com/antagomir/netresponse
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("netresponse")

Man pages

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
ICMg.combined.sampler: ICMg.combined.sampler
ICMg.get.comp.memberships: ICMg.get.comp.memberships
ICMg.links.sampler: ICMg.links.sampler
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
PlotMixtureMultivariate.deprecated: PlotMixtureMultivariate.deprecated
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
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.

Functions

AIC Source code
AICc Source code
BIC Source code
ICMg.combined.sampler Man page Source code
ICMg.get.comp.memberships Man page Source code Source code
ICMg.links.sampler Man page Source code
NetResponseModel-class Man page
P.S Man page Source code
P.Sr Man page Source code
P.r.s Man page Source code
P.rS Man page Source code
P.rs.joint Man page Source code
P.rs.joint.individual Man page Source code
P.s.individual Man page Source code
P.s.r Man page Source code
PlotMixture Man page Source code
PlotMixtureBivariate Man page Source code
PlotMixtureMultivariate Man page Source code
PlotMixtureMultivariate.deprecated Man page Source code
PlotMixtureUnivariate Man page Source code
[[,NetResponseModel-method Man page
add.ellipse Man page Source code
bic.mixture Man page Source code
bic.mixture.multivariate Man page Source code
bic.mixture.univariate Man page Source code
bic.select.best.mode Man page Source code
build.mim Source code
centerData Man page Source code
check.matrix Man page Source code
check.network Man page Source code
colVariances Source code
compute.weight Source code
continuous.responses Man page Source code
continuous.responses.single Source code
detect.responses Man page Source code
dna Man page
edge.delta Source code
ellipse Source code
enrichment.list Source code
enrichment.list.factor Man page Source code
enrichment.list.factor.minimal Man page Source code
enrichment.score Source code
factor.responses Man page Source code
factor.responses.minimal Man page Source code
filter.netw Man page Source code
filter.network Man page Source code
find.best.neighbor Source code
find.best.splitting Source code
find.similar.features Man page Source code
free.energy.improved Source code
fsort Source code
generate.toydata Man page Source code
get.dat Man page
get.dat,NetResponseModel-method Man page
get.mis Man page Source code
get.model.parameters Man page Source code
get.subnet Source code
get.subnets Man page
get.subnets,NetResponseModel-method Man page
getqofz Man page
getqofz,NetResponseModel-method Man page
greedy Source code
independent.models Man page Source code
info.criterion Source code
join.subnets Source code
list.responses.continuous.multi Man page Source code
list.responses.continuous.single Man page Source code
list.responses.factor Man page Source code
list.responses.factor.minimal Man page Source code
list.significant.responses Man page Source code
listify.groupings Man page Source code
mixture.model Man page Source code
mk.E.log.q.p.eta Source code
mk.free.energy Source code
mk.hp.posterior Source code
mk.hp.prior Source code
mk.log.lambda Source code
mk.qOFz Source code
model.stats Man page Source code
netresponse Man page
netresponse-package Man page
onAttach Source code
order.responses Man page Source code
osmo Man page
pick.model.pairs Man page Source code
pick.model.parameters Man page Source code
plotPCA Man page Source code
plot_associations Man page Source code
plot_data Man page Source code
plot_expression Man page Source code
plot_matrix Man page Source code
plot_response Man page Source code
plot_responses Man page Source code
plot_scale Man page Source code
plot_subnet Man page Source code
rand.qOFz Source code
read.sif Man page Source code
remove.negative.edges Man page Source code
response.enrichment Man page Source code
response2sample Man page Source code
retrieve.model Source code
sample2response Man page Source code
set.breaks Man page Source code
show,NetResponseModel-method Man page
softmax Source code
sortqofz Source code
split.qofz Source code
sumlogsumexp Source code
toydata Man page
update.model.pair Man page Source code
updatePosterior Source code
vdp.mixt Man page Source code
vectorize.groupings Man page Source code
write.netresponse.results Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/ICMg.R
R/ICMg.internals.R
R/NetResponseModel-accessors.R
R/PlotMixture.R
R/PlotMixtureUnivariate.R
R/add.ellipse.R
R/bic.mixture.R
R/bic.mixture.multivariate.R
R/bic.mixture.univariate.R
R/bic.select.best.mode.R
R/check.matrix.R
R/check.network.R
R/continuous.responses.R
R/deprecated.R
R/detect.responses.R
R/enrichment.list.R
R/enrichment.list.factor.R
R/enrichment.list.factor.minimal.R
R/enrichment.score.R
R/factor.responses.R
R/factor.responses.minimal.R
R/filter.netw.R
R/firstlib.R
R/get.mis.R
R/independent.models.R
R/information.criteria.R
R/internals.R
R/list.responses.continuous.R
R/list.responses.continuous.multi.R
R/list.responses.factor.R
R/list.responses.factor.minimal.R
R/listify.groupings.R
R/mixture.densities.R
R/mixture.model.R
R/model.stats.R
R/order.responses.R
R/pick.model.pairs.R
R/pick.model.parameters.R
R/pkg-package.R
R/plot-methods.R
R/plot_matrix.R
R/read.network.R
R/response.enrichment.R
R/response2sample.R
R/sample2response.R
R/show-methods.R
R/toydata.R
R/update.model.pair.R
R/utilities.R
R/vdp.mixt.R
R/visualization.R
README.md
data
data/dna.rda
data/osmo.rda
data/toydata.rda
inst
inst/CITATION
inst/NEWS
man
man/ICMg.combined.sampler.Rd
man/ICMg.get.comp.memberships.Rd
man/ICMg.links.sampler.Rd
man/NetResponseModel-class.Rd
man/P.S.Rd
man/P.Sr.Rd
man/P.r.s.Rd
man/P.rS.Rd
man/P.rs.joint.Rd
man/P.rs.joint.individual.Rd
man/P.s.individual.Rd
man/P.s.r.Rd
man/PlotMixture.Rd
man/PlotMixtureBivariate.Rd
man/PlotMixtureMultivariate.Rd
man/PlotMixtureMultivariate.deprecated.Rd
man/PlotMixtureUnivariate.Rd
man/add.ellipse.Rd
man/bic.mixture.Rd
man/bic.mixture.multivariate.Rd
man/bic.mixture.univariate.Rd
man/bic.select.best.mode.Rd
man/centerData.Rd
man/check.matrix.Rd
man/check.network.Rd
man/continuous.responses.Rd
man/detect.responses.Rd
man/dna.Rd
man/enrichment.list.factor.Rd
man/enrichment.list.factor.minimal.Rd
man/factor.responses.Rd
man/factor.responses.minimal.Rd
man/filter.netw.Rd
man/filter.network.Rd
man/find.similar.features.Rd
man/generate.toydata.Rd
man/get.dat-NetResponseModel-method.Rd
man/get.mis.Rd
man/get.model.parameters.Rd
man/get.subnets-NetResponseModel-method.Rd
man/getqofz-NetResponseModel-method.Rd
man/independent.models.Rd
man/list.responses.continuous.multi.Rd
man/list.responses.continuous.single.Rd
man/list.responses.factor.Rd
man/list.responses.factor.minimal.Rd
man/list.significant.responses.Rd
man/listify.groupings.Rd
man/mixture.model.Rd
man/model.stats.Rd
man/netresponse-package.Rd
man/order.responses.Rd
man/osmo.Rd
man/pick.model.pairs.Rd
man/pick.model.parameters.Rd
man/plotPCA.Rd
man/plot_associations.Rd
man/plot_data.Rd
man/plot_expression.Rd
man/plot_matrix.Rd
man/plot_response.Rd
man/plot_responses.Rd
man/plot_scale.Rd
man/plot_subnet.Rd
man/read.sif.Rd
man/remove.negative.edges.Rd
man/response.enrichment.Rd
man/response2sample.Rd
man/sample2response.Rd
man/set.breaks.Rd
man/toydata.Rd
man/update.model.pair.Rd
man/vdp.mixt.Rd
man/vectorize.groupings.Rd
man/write.netresponse.results.Rd
src
src/Makevars
src/netresponse.c
tests
tests/ICMg.test.R
tests/bicmixture.R
tests/mixture.model.test.R
tests/mixture.model.test.multimodal.R
tests/mixture.model.test.singlemode.R
tests/timing.R
tests/toydata2.R
tests/validate.netresponse.R
tests/validate.pca.basis.R
tests/vdpmixture.R
vignettes
vignettes/NetResponse.Rmd
vignettes/NetResponse.md
vignettes/TODO
vignettes/TODO/TODO.Rmd
vignettes/fig
vignettes/fig/NetResponse2-1.png
vignettes/fig/NetResponse2b-1.png
vignettes/fig/NetResponse3-1.png
vignettes/fig/NetResponse4-1.png
vignettes/fig/NetResponse5-1.png
vignettes/fig/NetResponse7-1.png
vignettes/fig/vdp-1.png
vignettes/main.R
vignettes/netresponse.bib
vignettes/netresponse.pdf
netresponse documentation built on May 20, 2017, 9:37 p.m.