subnetwork: Subnetwork

Description Usage Arguments Value Examples

View source: R/algorithm_functions.R

Description

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

Usage

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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

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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"))

pandaR documentation built on Nov. 1, 2018, 2:35 a.m.