subnetwork: Subnetwork

In QuackenbushLab/pandaR: PANDA Algorithm

Description

subnetwork gets a bipartite network containing only the transcription factors or genes and their respective connections

Usage

subnetwork(x, nodes, subTf = TRUE)

Arguments

x	an object of class "panda"
nodes	character vector containing the transcription factor or gene labels to subset
subTf	an optional logical indicating whether to subset by transcription factor. Default is TRUE.

Value

An matrix describing the subsetted bipartite network.

Examples

data(pandaToyData)
pandaRes <- panda(pandaToyData$motif,
           pandaToyData$expression,pandaToyData$ppi,hamming=.001,progress=TRUE)
topPandaRes <- topedges(pandaRes,1000)
subnet.pandaRes <- subnetwork(topPandaRes,c("AR","ARID3A","ELK1"))

data(pandaResult)
topPandaRes <- topedges(pandaResult,1000)
subnetwork(topPandaRes,c("AR","ARID3A","ELK1"))

QuackenbushLab/pandaR documentation built on May 8, 2019, 3:49 a.m.