calcDegree {pandaR} | R Documentation |
Calculates the transcription factor out-degree or gene in-degree for the estimated panda regulatory network.
calcDegree(x, type = c("tf", "gene"), filter = FALSE, trim = FALSE, ...)
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 |
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)