topedges {pandaR} | R Documentation |
topedges gets a network from a panda obj with a specified cutoff based on magnitude of edgeweight.
topedges(x, count = NA, cutoff = 2, networks = c("coregulation", "cooperation", "regulatory"))
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"). |
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)
data(pandaToyData) pandaRes <- panda(pandaToyData$motif, pandaToyData$expression,pandaToyData$ppi,hamming=.001,progress=TRUE) topPandaRes <- topedges(pandaRes,1000) data(pandaResult) topPandaRes <- topedges(pandaResult,1000)