internal.functions: internal.functions get.data plotmatrix get.gammashifted...

In ddepn: Dynamic Deterministic Effects Propagation Networks: Infer signalling networks for timecourse RPPA data.

Description

Some internal functions, usually not to be called directly.

Usage

get.data(gammax,mu.bg=0, sd.bg=0.1,
		mu.signal.a=1, sd.signal.a=0.5,
		mu.signal.i=-1, sd.signal.i=0.5,
		stimulus=NULL,TT=10,R.t=4,R.b=3)

plotmatrix(mat,name="")

get.gammashifted(gammax, partitions)

get.partitions(TT, npairs)

transitive.reduction(g)

transitive.closure(g, mat = FALSE, loops = TRUE)

tp.median(dat)

detailed.to.simple.regulations(phi)

reverse.direction(phi, i, switchtype=FALSE)

pad_data(dat)

order_experiments(dat)

get_reps_tps(nx)  

Arguments

Functions are usually not called directly.

gammax	todo
mu.bg, sd.bg, mu.signal.a, sd.signal.a, mu.signal.i, sd.signal.i	todo
stimulus	todo
R.t,R.b	todo
partitions	todo
mat	todo
name	todo
TT	todo
npairs	todo
g	todo
loops	todo
dat	todo
phi	todo
i	todo
switchtype	todo
nx	todo

Details

Some internal functions, usually not to be called directly. The code for transitive.reduction and transitive.closure was written by Holger Froehlich and is published in the R-package 'nem' available on bioconductor. However, to avoid forcing to load the rather big package 'nem' the code is included in this package, too.

Value

none

Author(s)

Christian Bender

ddepn documentation built on May 2, 2019, 4:42 p.m.