topedges: Top edges

Description Usage Arguments Value Examples

Description

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

Usage

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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

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

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


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