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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("BioNet")
AuthorMarcus Dittrich and Daniela Beisser
Bioconductor views DataImport DifferentialExpression GeneExpression GraphAndNetwork Microarray Network NetworkEnrichment
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

Functions

aggrPvals Man page
BioNet Man page
BioNet-package Man page
bumOptim Man page
compareNetworks Man page
consensusScores Man page
fbum Man page
fbumLL Man page
fdrThreshold Man page
fitBumModel Man page
getCompScores Man page
getEdgeList Man page
hist.bum Man page
largestComp Man page
largestScoreComp Man page
loadNetwork.sif Man page
loadNetwork.tab Man page
makeNetwork Man page
mapByVar Man page
permutateNodes Man page
piUpper Man page
plot3dModule Man page
plot.bum Man page
plotLLSurface Man page
plotModule Man page
print.bum Man page
pvaluesExample Man page
readHeinzGraph Man page
readHeinzTree Man page
resamplingPvalues Man page
rmSelfLoops Man page
runFastHeinz Man page
runHeinz Man page
save3dModule Man page
saveNetwork Man page
scanFDR Man page
scoreFunction Man page
scoreNodes Man page
scoreOffset Man page
sortedEdgeList Man page
subNetwork Man page
summary.bum Man page
writeHeinz Man page
writeHeinzEdges Man page
writeHeinzNodes Man page

Files

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

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

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