calcDegreeDifference: Calculate difference in degrees

Description Usage Arguments Examples

Description

Calculates the transcription factor out-degree or gene in-degree for two different panda regulatory networks. This is useful in comparing networks from two phenotypes.

Usage

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

Arguments

x

An object of class "panda" or matrix

y

A second 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

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data(pandaToyData)
pandaRes <- panda(pandaToyData$motif,
           pandaToyData$expression,pandaToyData$ppi,hamming=.001,progress=TRUE)
pandaRes2 <- panda(pandaToyData$motif,
           pandaToyData$expression,pandaToyData$ppi,hamming=.1,progress=TRUE)
calcDegreeDifference(pandaRes,pandaRes2)
calcDegreeDifference(pandaRes,pandaRes2,trim=TRUE,cutoff=1.5)


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