Package: BioNet 1.73.0

Marcus Dittrich

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.

Authors:Marcus Dittrich and Daniela Beisser

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
BioNet/json (API)

# Install 'BioNet' in R:

install.packages('BioNet', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

pvaluesExample - Example p-values for aggregation statistics

On BioConductor:BioNet-1.73.0(bioc 3.24)BioNet-1.72.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

microarray dataimport graphandnetwork network networkenrichment geneexpression differentialexpression

6.32 score 2 packages 173 scripts 40 mentions 42 exports 42 dependencies

Last updated from:52d7a61b57. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	190
linux-devel-x86_64	NOTE	341
source / vignettes	OK	303
linux-release-x86_64	NOTE	290
macos-release-arm64	NOTE	149
macos-oldrel-arm64	NOTE	155
windows-devel	NOTE	237
windows-release	NOTE	246
windows-oldrel	NOTE	230
wasm-release	OK	160

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

Dependencies:AnnotationDbi askpass BH Biobase BiocGenerics Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI fastmap generics glue graph httr igraph IRanges jsonlite KEGGREST lattice lifecycle magrittr Matrix memoise mime openssl pkgconfig png R6 RBGL rlang RSQLite S4Vectors Seqinfo sys vctrs XVector

BioNet Tutorial

Rendered fromTutorial.Rnwusingutils::Sweave

Last update: 2020-10-05
Started: 2013-11-01

Help page	Topics
Routines for the functional analysis of biological networks	BioNet-package BioNet
Aggregate several p-values into one p-value	aggrPvals
Fitting a beta-uniform mixture model to p-value distribution	bumOptim
Compare parameters of two networks	compareNetworks
Calculation of a consensus score for a network	consensusScores
Compute the density of the bum distribution	fbum
Calculate log likelihood of BUM model	fbumLL
Calculate p-value threshold for given FDR	fdrThreshold
Fit beta-uniform mixture model to a p-value distribution	fitBumModel
Partition scores for subgraphs of the network	getCompScores
Get representation of graph as edgelist	getEdgeList
Histogram of the p-value distribution with the fitted bum model	hist.bum
Extract largest component of network	largestComp
Component with largest score	largestScoreComp
Load network from Cytoscape sif file	loadNetwork.sif
Load network from tabular format	loadNetwork.tab
Create graph from source and target vectors	makeNetwork
Select probeset by variance and get PPI ID	mapByVar
Permute node labels	permutateNodes
Upper bound pi for the fraction of noise	piUpper
Quantile-quantile plot for the beta-uniform mixture model	plot.bum
3D plot of the network	plot3dModule
Log likelihood surface plot	plotLLSurface
Plot of the network	plotModule
Print information about bum model	print.bum
Example p-values for aggregation statistics	pvaluesExample
Convert HEINZ output to graph	readHeinzGraph
Convert HEINZ output to tree	readHeinzTree
Resampling of microarray expression values and test for differential expression.	resamplingPvalues
Remove self-loops in a graph	rmSelfLoops
Calculate heuristically maximum scoring subnetwork	runFastHeinz
Start HEINZ	runHeinz
Save a 3D plot of the network	save3dModule
Save undirected network in various formats	saveNetwork
Dataframe of scores over a given range of FDRs	scanFDR
Scoring function for p-values	scoreFunction
Score the nodes of a network	scoreNodes
Change score offset for 2 FDRs	scoreOffset
Get a sorted edgelist	sortedEdgeList
Create a subGraph	subNetwork
Print summary of informations about bum model	summary.bum
Write input files for HEINZ	writeHeinz
Write edge input file for HEINZ	writeHeinzEdges
Write node input file for HEINZ	writeHeinzNodes

Package: BioNet 1.73.0

BioNet: Routines for the functional analysis of biological networks

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