calcDegreeDifference {pandaR} | R Documentation |
Calculates the transcription factor out-degree or gene in-degree for two different panda regulatory networks. This is useful in comparing networks from two phenotypes.
calcDegreeDifference(x, y, type = c("tf", "gene"), filter = FALSE, trim = FALSE, ...)
x |
An object of class "panda" or matrix |
y |
A second 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$ppi,hamming=.001,progress=TRUE) pandaRes2 <- panda(pandaToyData$motif, pandaToyData$expression,pandaToyData$ppi,hamming=.1,progress=TRUE) calcDegreeDifference(pandaRes,pandaRes2) calcDegreeDifference(pandaRes,pandaRes2,trim=TRUE,cutoff=1.5)