estimateNetwork: Estimate network between active regulators using Nested...

In birte: Bayesian Inference of Regulatory Influence on Expression (biRte)

Description

Given a biRte model, this function makes posterior inference about possible upstream-downstream relationships between active regulators. This is done based on observed differential expression of putative target genes. The idea is that regulator A acts upstream of regulator B, if differentially expressed targets of B are a subset of those of A.

Usage

estimateNetwork(model, thresh=0.1, select=c("marginal", "MAP"), method="pairwise",
de.genes, bootstrap=0, typeII=0.1)

Arguments

model	biRte model
thresh	cutoff for marginal posterior probabilities
select	"marginal": select regulators based on marginal posterior probabilities; "MAP": select regulators based on MAP configuration
method	algorithm used for NEM based network inference, see nem
de.genes	set of differentially expressed genes
bootstrap	optional: number of bootstrap replicates to draw (non-parameteric bootstrap)
typeII	assumed type-II error rate

Value

nem-model

Author(s)

Holger Froehlich

Examples

# see vignette

birte documentation built on May 2, 2019, 12:32 a.m.