topedges: Top edges

In jnpaulson/pandaR: PANDA Algorithm

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)

jnpaulson/pandaR documentation built on Oct. 1, 2023, 3:14 a.m.