predictionet: Inference for predictive networks designed for (but not limited to) genomic data

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This package contains a set of functions related to network inference combining genomic data and prior information extracted from biomedical literature and structured biological databases. The main function is able to generate networks using Bayesian or regression-based inference methods; while the former is limited to < 100 of variables, the latter may infer networks with hundreds of variables. Several statistics at the edge and node levels have been implemented (edge stability, predictive ability of each node, ...) in order to help the user to focus on high quality subnetworks. Ultimately, this package is used in the 'Predictive Networks' web application developed by the Dana-Farber Cancer Institute in collaboration with Entagen.

Author
Benjamin Haibe-Kains, Catharina Olsen, Gianluca Bontempi, John Quackenbush
Date of publication
None
Maintainer
Benjamin Haibe-Kains <bhaibeka@jimmy.harvard.edu>, Catharina Olsen <colsen@ulb.ac.be>
License
Artistic-2.0
Version
1.20.0
URLs

View on Bioconductor

Man pages

adj.get.hops
Function to identify all children of a parent
adj.remove.cycles
Function to remove cycles that may be present in a directed...
data.discretize
Function to discretize data based on user specified cutoffs
eval.network
Function computing the f1-score, comparing an inferred...
expO.colon.ras
Gene expression, annotations, clinical data and priors for...
jorissen.colon.ras
Gene expression, annotations, clinical data and priors for...
mcc
Function to compute the Matthews Correlation Coefficient...
net2pred
Function fitting a regression model for each gene in the data
netinf
Function performing network inference by combining priors and...
netinf2gml
Function to create an 'igraph' object and export a network to...
netinf.cv
Function performing network inference by combining priors and...
netinf.predict
Function to make prediction of a node values given its...
predictionet-package
Inference for predictive networks designed for (but not...
predictionet.press.statistic
Function computing the press statistic for all target...
predictionet.stability.cv
Function inferring networks in cross-validation
pred.score
Function computing performance of prediction; methods include...

Files in this package

predictionet/.BBSoptions
predictionet/DESCRIPTION
predictionet/NAMESPACE
predictionet/R
predictionet/R/adj.get.hops.R
predictionet/R/adj.remove.cycles.R
predictionet/R/build.regression.regrnet.R
predictionet/R/build2.mim.R
predictionet/R/data.discretize.R
predictionet/R/eval.network.R
predictionet/R/exportGML.R
predictionet/R/extract.adjacency.ensemble.R
predictionet/R/extract.all.parents.R
predictionet/R/fit.catnet.R
predictionet/R/fit.regrnet.causal.R
predictionet/R/fit.regrnet.causal.ensemble.R
predictionet/R/fit.regrnet.causal2.R
predictionet/R/get.ii4triplets.gaussian.R
predictionet/R/list2matrixens.R
predictionet/R/mcc.R
predictionet/R/net2pred.R
predictionet/R/netinf.R
predictionet/R/netinf.cv.R
predictionet/R/netinf.predict.R
predictionet/R/netinf2gml.R
predictionet/R/network2triplets.R
predictionet/R/pred.onegene.bayesnet.fs.R
predictionet/R/pred.onegene.regrnet.fs.R
predictionet/R/pred.score.R
predictionet/R/pred2mean.R
predictionet/R/predictionet.press.statistic.R
predictionet/R/predictionet.stability.cv.R
predictionet/R/rank.genes.causal.ensemble.R
predictionet/R/rank.genes.causal.perturbations.R
predictionet/R/rank.genes.causal.perturbations2.R
predictionet/R/rank.genes.ensemble.R
predictionet/R/regrlin.R
predictionet/R/regrnet2matrixtopo.R
predictionet/R/stab.cv2stab.R
predictionet/R/topo2stab.R
predictionet/README
predictionet/build
predictionet/build/predictionet.pdf
predictionet/build/vignette.rds
predictionet/data
predictionet/data/datalist
predictionet/data/expO.colon.ras.rda
predictionet/data/jorissen.colon.ras.rda
predictionet/inst
predictionet/inst/doc
predictionet/inst/doc/predictionet.R
predictionet/inst/doc/predictionet.Rnw
predictionet/inst/doc/predictionet.pdf
predictionet/inst/extdata
predictionet/inst/extdata/bild2006_ras_signature_348.csv
predictionet/inst/extdata/preditionet_vizmap1.props
predictionet/inst/extdata/preditionet_vizmap2.props
predictionet/inst/extdata/priors_ras_bild2006_pnwebapp.csv
predictionet/man
predictionet/man/adj.get.hops.Rd
predictionet/man/adj.remove.cycles.Rd
predictionet/man/data.discretize.Rd
predictionet/man/eval.network.Rd
predictionet/man/expO.colon.ras.Rd
predictionet/man/jorissen.colon.ras.Rd
predictionet/man/mcc.Rd
predictionet/man/net2pred.Rd
predictionet/man/netinf.Rd
predictionet/man/netinf.cv.Rd
predictionet/man/netinf.predict.Rd
predictionet/man/netinf2gml.Rd
predictionet/man/pred.score.Rd
predictionet/man/predictionet-package.Rd
predictionet/man/predictionet.press.statistic.Rd
predictionet/man/predictionet.stability.cv.Rd
predictionet/src
predictionet/src/foo_mrmr.cpp
predictionet/src/foo_mrmr.h
predictionet/src/mrnet_adapted.cpp
predictionet/src/mrnet_adapted2.cpp
predictionet/src/mrnet_ensemble_standalone.cpp
predictionet/src/tree.h
predictionet/vignettes
predictionet/vignettes/biblio.bib
predictionet/vignettes/predictionet-cytoscape.pdf
predictionet/vignettes/predictionet-pn_webapp_ras.pdf
predictionet/vignettes/predictionet-regrnet_design.pdf
predictionet/vignettes/predictionet.Rnw