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.

Author
Marcus Dittrich and Daniela Beisser
Date of publication
None
Maintainer
Marcus Dittrich <marcus.dittrich@biozentrum.uni-wuerzburg.de>
License
GPL (>= 2)
Version
1.34.0
URLs

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