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. |