networkBMA (version 1.14.0)

Regression-based network inference using Bayesian Model Averaging

Description

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

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Version

1.14.0

License

GPL (>= 2)

Maintainer

Ka Yeung

Last Published

February 15th, 2017

Functions in networkBMA (1.14.0)

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.

iterateBMAlm

Iterative BMA for linear modeling with prior variable probabilities.

roc

Receiver Operating Characteristic and Precision-Recall Curves

contabs.prelim

Preliminary calculation for network assessment.

ScanBMA

Bayesian Model Averaging for linear regression models.

dream4

DREAM 4 (Stolovitsky et al. 2007) `gold standard' reference network specifications, simulated time series perturbation subsets, and steady state (wild-type) gene expression levels.

ScanBMAcontrol

Control parameters for ScanBMA

scores

Scores for assessment from contingency tables.

iBMAcontrolLM

Control parameters for iterateBMAlm

network-internal

Internal functions for the networkBMA package

varord

Variable orderings for linear regression.

gControl

Control parameters for using Zellner's g-prior in ScanBMA

networkBMA

Gene network inference from time series data via BMA.

contabs.netwBMA

Network assessment with incomplete context.

contabs

Contingency tables for networks with probabilistic edges.

summary.networkBMA

Summarizes a networkBMA object.