networkBMA: Regression-based network inference using Bayesian Model Averaging
Version 2.16.1

An extension of Bayesian Model Averaging (BMA) for network construction using time series gene expression data. Includes assessment functions and sample test data.

Browse man pages Browse package API and functions Browse package files

AuthorChris Fraley, Wm. Chad Young, Ling-Hong Hung, Kaiyuan Shi, Ka Yee Yeung, Adrian Raftery (with contributions from Kenneth Lo)
Bioconductor views Bayesian GeneExpression GeneTarget GraphsAndNetwork Network NetworkInference
Date of publicationNone
MaintainerKa Yee Yeung <kayee@u.washington.edu>
LicenseGPL (>= 2)
Version2.16.1
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("networkBMA")

Man pages

contabs: Contingency tables for networks with probabilistic edges.
contabs.netwBMA: Network assessment with incomplete context.
contabs.prelim: Preliminary calculation for network assessment.
dream4: DREAM 4 (Stolovitsky et al. 2007) 'gold standard' reference...
fastBMAcontrol: Control parameters for 'networkBMA' when using fastBMA...
fastgControl: Control parameters for using Zellner's g-prior in fastBMA...
gControl: Control parameters for using Zellner's g-prior in 'ScanBMA'
iBMAcontrolLM: Control parameters for 'iterateBMAlm'
iterateBMAlm: Iterative BMA for linear modeling with prior variable...
networkBMA: Gene network inference from time series data via BMA.
networkBMA-internal: Internal functions for the networkBMA package
roc: Receiver Operating Characteristic and Precision-Recall Curves
ScanBMA: Bayesian Model Averaging for linear regression models.
ScanBMAcontrol: Control parameters for 'ScanBMA'
scores: Scores for assessment from contingency tables.
summary.networkBMA: Summarizes a 'networkBMA' object.
varord: Variable orderings for linear regression.
vignette: The subsets of the yeast-rapamycin time-series data from...
writeEdges: Output network edges to text in Cytoscape-readable format.

Functions

BMA.Diff.BIC Source code
BMA.Diff.g Source code
BMA_Diff_BIC Source code
BMA_Diff_g Source code
FastScanBMA.BIC Source code
FastScanBMA.g Source code
Optimizeg Source code
ScanBMA Man page Source code
ScanBMA.BIC Source code
ScanBMA.g Source code
ScanBMA_BIC Source code
ScanBMA_g Source code
ScanBMAcontrol Man page Source code
bicreg.pr Man page Source code
bicreg.pr.resid Man page Source code
brem.data Man page
contabs Man page Source code
contabs.netwBMA Man page Source code
contabs.prelim Man page Source code
dream4gold10 Man page
dream4gold100 Man page
dream4ts10 Man page
dream4ts100 Man page
dream4wild10 Man page
dream4wild100 Man page
fastBMA Source code
fastBMA_g Source code
fastBMAcontrol Man page Source code
fastgControl Man page Source code
gControl Man page Source code
iBMAcontrolLM Man page Source code
iterateBMA.resid Man page
iterateBMAlm Man page Source code
iterateBMAlm.resid Source code
list2df Man page Source code
matrixFormat Man page Source code
networkBMA Man page Source code
networkBMA.old Source code
prc Man page Source code
refNetwCalc Source code
referencePairs Man page
reg.known Man page
reg.prob Man page
roc Man page Source code
scores Man page Source code
summary.networkBMA Man page
timeSeries Man page
varord Man page
vignette Man page
writeEdges Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/FastScanBMABIC.r
R/FastScanBMAg.r
R/RcppExports.R
R/ScanBMA.R
R/ScanBMABIC.r
R/ScanBMAcontrol.R
R/ScanBMAg.r
R/bicreg.pr.R
R/bicreg.pr.resid.R
R/contabs.R
R/contabs.netwBMA.R
R/contabs.prelim.R
R/fastBMA.R
R/fastBMAcontrol.R
R/iBMAcontrolLM.R
R/iterateBMAlm.R
R/iterateBMAlm.resid.R
R/list2df.R
R/matrixFormat.R
R/networkBMA.R
R/prc.R
R/refNetwCalc.R
R/roc.R
R/scores.R
R/summary.networkBMA.R
R/varord.R
R/writeEdges.R
build
build/vignette.rds
data
data/datalist
data/dream4.rda
data/vignette.rda
inst
inst/CITATION
inst/cite
inst/doc
inst/doc/networkBMA.R
inst/doc/networkBMA.Rnw
inst/doc/networkBMA.pdf
inst/unitTests
man
man/ScanBMA.Rd
man/ScanBMAcontrol.Rd
man/contabs.Rd
man/contabs.netwBMA.Rd
man/contabs.prelim.Rd
man/dream4.Rd
man/fastBMAcontrol.Rd
man/fastgControl.Rd
man/gControl.Rd
man/iBMAcontrolLM.Rd
man/iterateBMAlm.Rd
man/networkBMA-internal.Rd
man/networkBMA.Rd
man/roc.Rd
man/scores.Rd
man/summary.networkBMA.Rd
man/varord.Rd
man/vignette.Rd
man/writeEdges.Rd
networkBMA.Rproj
src
src/Makevars
src/Makevars.in
src/Makevars.win
src/MurmurHash3.cpp
src/MurmurHash3.h
src/RcppExports.cpp
src/ScanBMA_full.cpp
src/bmaNoMPI.hpp
src/config.h
src/config.h.in
src/fastBMA.hpp
src/fastBMAR.cpp
src/include
src/include/blas.h
src/include/lapacke.h
src/include/lapacke_config.h
src/include/lapacke_mangling.h
src/include/lapacke_utils.h
src/my_sort.hpp
vignettes
vignettes/algorithm2e.sty
vignettes/networkBMA.Rnw
vignettes/networkBMA.bib
vignettes/prc-update.pdf
vignettes/relsize.sty
vignettes/roc-update.pdf
networkBMA documentation built on May 20, 2017, 10:57 p.m.