# Regression-based network inference using Bayesian Model Averaging

## Documentation for package ‘networkBMA’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

brem.data | The subsets of the yeast-rapamycin time-series data from Yeung et al. (2011) and Lo et al. (2011), and of the static yeast gene-expression data from Brem et al. (2002, 2005), that are used in the 'networkBMA' package vignette.
contabs | Contingency tables for networks with probabilistic edges.
contabs.netwBMA | Network assessment with incomplete context.
contabs.prelim | Preliminary calculation for network assessment.
dream4gold10 | DREAM 4 (Stolovitsky et al. 2007) 'gold standard' reference network specifications, simulated time series perturbation subsets, and steady state (wild-type) gene expression levels.
dream4gold100 | DREAM 4 (Stolovitsky et al. 2007) 'gold standard' reference network specifications, simulated time series perturbation subsets, and steady state (wild-type) gene expression levels.
dream4ts10 | DREAM 4 (Stolovitsky et al. 2007) 'gold standard' reference network specifications, simulated time series perturbation subsets, and steady state (wild-type) gene expression levels.
dream4ts100 | DREAM 4 (Stolovitsky et al. 2007) 'gold standard' reference network specifications, simulated time series perturbation subsets, and steady state (wild-type) gene expression levels.
dream4wild10 | DREAM 4 (Stolovitsky et al. 2007) 'gold standard' reference network specifications, simulated time series perturbation subsets, and steady state (wild-type) gene expression levels.
dream4wild100 | DREAM 4 (Stolovitsky et al. 2007) 'gold standard' reference network specifications, simulated time series perturbation subsets, and steady state (wild-type) gene expression levels.
iBMAcontrolLM | Control parameters for 'iterateBMAlm'
iterateBMAlm | Iterative BMA for linear modeling with prior variable probabilities.
matrixFormat | Contingency tables for networks with probabilistic edges.
networkBMA | Gene network inference from time series data via BMA.
prc | Receiver Operating Characteristic and Precision-Recall Curves
referencePairs | The subsets of the yeast-rapamycin time-series data from Yeung et al. (2011) and Lo et al. (2011), and of the static yeast gene-expression data from Brem et al. (2002, 2005), that are used in the 'networkBMA' package vignette.
reg.known | The subsets of the yeast-rapamycin time-series data from Yeung et al. (2011) and Lo et al. (2011), and of the static yeast gene-expression data from Brem et al. (2002, 2005), that are used in the 'networkBMA' package vignette.
reg.prob | The subsets of the yeast-rapamycin time-series data from Yeung et al. (2011) and Lo et al. (2011), and of the static yeast gene-expression data from Brem et al. (2002, 2005), that are used in the 'networkBMA' package vignette.
roc | Receiver Operating Characteristic and Precision-Recall Curves
scores | Scores for assessment from contingency tables.
summary.networkBMA | Summarizes a 'networkBMA' object.
timeSeries | The subsets of the yeast-rapamycin time-series data from Yeung et al. (2011) and Lo et al. (2011), and of the static yeast gene-expression data from Brem et al. (2002, 2005), that are used in the 'networkBMA' package vignette.
varord | Variable orderings for linear regression.
vignette | The subsets of the yeast-rapamycin time-series data from Yeung et al. (2011) and Lo et al. (2011), and of the static yeast gene-expression data from Brem et al. (2002, 2005), that are used in the 'networkBMA' package vignette.
writeEdges | Output network edges to text in Cytoscape-readable format.