Estimate network between active regulators using Nested Effects Models (NEMs).

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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

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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

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# see vignette