topedges {pandaR} | R Documentation

## Top edges

### Description

topedges gets a network from a panda obj with a specified cutoff based on magnitude of edgeweight.

### Usage

    topedges(x, count = NA, cutoff = 2, networks = c("coregulation",
      "cooperation", "regulatory"))

### Arguments

`x` | an object of class "panda"
`count` | an optional integer indicating number of top edges to be included in regulatory network.
`cutoff` | an optional numeric indicating the z-score edge weight cutoff to be used to identify edges. Default is 2.0. Not used if count is not NA.
`networks` | an optional vector specifying which networks to be included in output. May be any combination of c("coregulation","cooperation","regulatory").

### Value

An object of class "panda" containing binary matrices indicating the existence of an edge between two nodes. For regulatory network the matrix indicates an edge between a transcription factor (row) and a gene (column)

### Examples

    data(pandaToyData)
    pandaRes <- panda(pandaToyData$motif,
               pandaToyData$expression,pandaToyData$ppi,hamming=.001,progress=TRUE)
    topPandaRes <- topedges(pandaRes,1000)

    data(pandaResult)
    topPandaRes <- topedges(pandaResult,1000)

[Package pandaR version 1.18.0 Index]