calcDegreeDifference {pandaR} | R Documentation

## 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)

[Package pandaR version 1.16.0 Index]