Bayesian Inference of Regulatory Influence on Expression (biRte)


[Up] [Top]

Documentation for package ‘birte’ version 1.12.0

Help Pages

affinities2 Subset of regulator-target gene network for human
birteFitRidge Fit ridge regression model given a defined set of active regulators.
birteLimma Main interface for Bayesian Inference of Regulatory Influence on Expression (biRte).
birtePredict Prediction of gene expression via biRte.
birteRun Main interface for Bayesian Inference of Regulatory Influence on Expression (biRte).
EColiNetwork Example TF-target graph from Regulon DB.
EColiOxygen Example data set from E. Coli to sample TF activities.
estimateNetwork Estimate network between active regulators using Nested Effects Models (NEMs).
getPotentialSwaps Calculate swap partner for TF-/miRNA-target graph. This function is usually only called internally, but may be used to speed up repetitive calls to 'birteRun'.
humanNetworkSimul Subset of regulator-target gene network for human
limmaAnalysis Simple limma analysis on expression data with one contrast.
plotConvergence Plot the marginal log-likelihood of the model along MCMC samples (after thinning).
proposeInteractions Propose possible regulator-regulator interactions that could be worthwhile to be tested into the biRte model.
simplify Simplify regulator-target gene network via clustering.
simulateData Simulate expression data.
suggestThreshold Automatically suggest suitable threshold for marginal regulator activities.
TFexpr Transcription factor expression values for the aerobic-anaerobic growth experiment.