calcDegree {pandaR} | R Documentation

## Calculate regulatory network degree

### 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)

[Package pandaR version 1.26.0 Index]