estimateNetwork {birte} | R Documentation |
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.
estimateNetwork(model, thresh=0.1, select=c("marginal", "MAP"), method="pairwise", de.genes, bootstrap=0, typeII=0.1)
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 |
de.genes |
set of differentially expressed genes |
bootstrap |
optional: number of bootstrap replicates to draw (non-parameteric bootstrap) |
typeII |
assumed type-II error rate |
nem-model
Holger Froehlich
# see vignette