calcDegreeDifference: Calculate difference in degrees

In jnpaulson/pandaR: PANDA Algorithm

Calculate difference in degrees

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

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

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)

jnpaulson/pandaR documentation built on May 13, 2024, 11:30 a.m.