calcDegree: Calculate regulatory network degree

In QuackenbushLab/pandaR: PANDA Algorithm

Description

Calculates the transcription factor out-degree or gene in-degree for the estimated panda regulatory network.

Usage

calcDegree(x, type = c("tf", "gene"), filter = FALSE, trim = FALSE, ...)

Arguments

x	An object of class "panda" or matrix
type	Character string - 'tf' or 'gene'
filter	Boolean to force negative degrees to zero
trim	Boolean to trim using topedges or not at a cutoff (weights become binary 1,0)
...	Options to be passed to topedges function

Examples

data(pandaToyData)
pandaRes <- panda(pandaToyData$motif,
           pandaToyData$expression,pandaToyData$ppi,hamming=.001,progress=TRUE)
calcDegree(pandaRes)
calcDegree(pandaRes,trim=TRUE,cutoff=1.5)

data(pandaResult)
calcDegree(pandaResult,type="tf",trim=TRUE,1000)
calcDegree(pandaResult,type="gene",trim=TRUE,1000)

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