BioNet: Routines for the functional analysis of biological networks

This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. E.g. p-values obtained from the differential expression of the genes from an Affymetrix array are assigned to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from the p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork.

AuthorMarcus Dittrich and Daniela Beisser
Date of publicationNone
MaintainerMarcus Dittrich <marcus.dittrich@biozentrum.uni-wuerzburg.de>
LicenseGPL (>= 2)
Version1.34.0
http://bionet.bioapps.biozentrum.uni-wuerzburg.de/

View on Bioconductor

Man pages

aggrPvals: Aggregate several p-values into one p-value

BioNet-package: Routines for the functional analysis of biological networks

bumOptim: Fitting a beta-uniform mixture model to p-value distribution

compareNetworks: Compare parameters of two networks

consensusScores: Calculation of a consensus score for a network

fbum: Compute the density of the bum distribution

fbumLL: Calculate log likelihood of BUM model

fdrThreshold: Calculate p-value threshold for given FDR

fitBumModel: Fit beta-uniform mixture model to a p-value distribution

getCompScores: Partition scores for subgraphs of the network

getEdgeList: Get representation of graph as edgelist

hist.bum: Histogram of the p-value distribution with the fitted bum...

largestComp: Extract largest component of network

largestScoreComp: Component with largest score

loadNetwork.sif: Load network from Cytoscape sif file

loadNetwork.tab: Load network from tabular format

makeNetwork: Create graph from source and target vectors

mapByVar: Select probeset by variance and get PPI ID

permutateNodes: Permute node labels

piUpper: Upper bound pi for the fraction of noise

plot3dModule: 3D plot of the network

plot.bum: Quantile-quantile plot for the beta-uniform mixture model

plotLLSurface: Log likelihood surface plot

plotModule: Plot of the network

print.bum: Print information about bum model

pvaluesExample: Example p-values for aggregation statistics

readHeinzGraph: Convert HEINZ output to graph

readHeinzTree: Convert HEINZ output to tree

resamplingPvalues: Resampling of microarray expression values and test for...

rmSelfLoops: Remove self-loops in a graph

runFastHeinz: Calculate heuristically maximum scoring subnetwork

runHeinz: Start HEINZ

save3dModule: Save a 3D plot of the network

saveNetwork: Save undirected network in various formats

scanFDR: Dataframe of scores over a given range of FDRs

scoreFunction: Scoring function for p-values

scoreNodes: Score the nodes of a network

scoreOffset: Change score offset for 2 FDRs

sortedEdgeList: Get a sorted edgelist

subNetwork: Create a subGraph

summary.bum: Print summary of informations about bum model

writeHeinz: Write input files for HEINZ

writeHeinzEdges: Write edge input file for HEINZ

writeHeinzNodes: Write node input file for HEINZ

Files in this package

BioNet/DESCRIPTION
BioNet/NAMESPACE
BioNet/R
BioNet/R/Graph.R BioNet/R/HeinzUtils.R BioNet/R/IO.R BioNet/R/MAUtils.R BioNet/R/Plots.R BioNet/R/Resampling.R BioNet/R/Statistics.R
BioNet/build
BioNet/build/vignette.rds
BioNet/data
BioNet/data/pvaluesExample.rda
BioNet/inst
BioNet/inst/CITATION
BioNet/inst/doc
BioNet/inst/doc/Tutorial.R
BioNet/inst/doc/Tutorial.Rnw
BioNet/inst/doc/Tutorial.pdf
BioNet/inst/extdata
BioNet/inst/extdata/ALL_cons_n.txt.0.hnz
BioNet/inst/extdata/ALL_edges_001.txt.0.hnz
BioNet/inst/extdata/ALL_n_resample.txt.0.hnz
BioNet/inst/extdata/ALL_nodes_001.txt.0.hnz
BioNet/inst/extdata/cytoscape.sif
BioNet/inst/extdata/lymphoma_edges_001.txt.0.hnz
BioNet/inst/extdata/lymphoma_nodes_001.txt.0.hnz
BioNet/inst/extdata/n.weight.NA
BioNet/inst/extdata/weight.EA
BioNet/man
BioNet/man/BioNet-package.Rd BioNet/man/aggrPvals.Rd BioNet/man/bumOptim.Rd BioNet/man/compareNetworks.Rd BioNet/man/consensusScores.Rd BioNet/man/fbum.Rd BioNet/man/fbumLL.Rd BioNet/man/fdrThreshold.Rd BioNet/man/fitBumModel.Rd BioNet/man/getCompScores.Rd BioNet/man/getEdgeList.Rd BioNet/man/hist.bum.Rd BioNet/man/largestComp.Rd BioNet/man/largestScoreComp.Rd BioNet/man/loadNetwork.sif.Rd BioNet/man/loadNetwork.tab.Rd BioNet/man/makeNetwork.Rd BioNet/man/mapByVar.Rd BioNet/man/permutateNodes.Rd BioNet/man/piUpper.Rd BioNet/man/plot.bum.Rd BioNet/man/plot3dModule.Rd BioNet/man/plotLLSurface.Rd BioNet/man/plotModule.Rd BioNet/man/print.bum.Rd BioNet/man/pvaluesExample.Rd BioNet/man/readHeinzGraph.Rd BioNet/man/readHeinzTree.Rd BioNet/man/resamplingPvalues.Rd BioNet/man/rmSelfLoops.Rd BioNet/man/runFastHeinz.Rd BioNet/man/runHeinz.Rd BioNet/man/save3dModule.Rd BioNet/man/saveNetwork.Rd BioNet/man/scanFDR.Rd BioNet/man/scoreFunction.Rd BioNet/man/scoreNodes.Rd BioNet/man/scoreOffset.Rd BioNet/man/sortedEdgeList.Rd BioNet/man/subNetwork.Rd BioNet/man/summary.bum.Rd BioNet/man/writeHeinz.Rd BioNet/man/writeHeinzEdges.Rd BioNet/man/writeHeinzNodes.Rd
BioNet/vignettes
BioNet/vignettes/Tutorial-3dplot.pdf
BioNet/vignettes/Tutorial.Rnw
BioNet/vignettes/Tutorials.bib
BioNet/vignettes/bum1.pdf
BioNet/vignettes/bum2.pdf
BioNet/vignettes/cytoscape.pdf
BioNet/vignettes/prec_recall_large.pdf
BioNet/vignettes/prec_recall_small.pdf

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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