moduleNetwork {nem} | R Documentation |
Function moduleNetwork
estimates the hierarchy using a divide and conquer approach. In each step only a subset of nodes (called module)
is involved and no exhaustive enumeration of model space is needed as in function score
.
moduleNetwork(D,type="mLL",Pe=NULL,Pm=NULL,lambda=0,delta=1,para=NULL,hyperpara=NULL,verbose=TRUE) ## S3 method for class 'ModuleNetwork': print(x,...)
D |
data matrix. Columns correspond to the nodes in the silencing scheme. Rows are phenotypes. |
type |
(1.) marginal likelihood "mLL" (only for cout matrix D), or (2.) full marginal likelihood "FULLmLL" integrated over a and b and depending on hyperparameters a0, a1, b0, b1 (only for count matrix D), or (3.) "CONTmLL" marginal likelihood for probability matrices, or (4.) "CONTmLLDens" marginal likelihood for probability density matrices, or (5.) "CONTmLLRatio" for log-odds ratio matrices |
Pe |
prior position of effect reporters. Default: uniform over nodes in hierarchy |
Pm |
prior on model graph (n x n matrix) with entries 0 <= priorPhi[i,j] <= 1 describing the probability of an edge between gene i and gene j. |
lambda |
regularization parameter to incorporate prior assumptions. |
delta |
regularization parameter for automated E-gene subset selection (CONTmLLRatio only) |
para |
vector with parameters a and b for "mLL", if count matrices are used |
hyperpara |
vector with hyperparameters a0, b0, a1, b1 for "FULLmLL" |
verbose |
do you want to see progress statements printed or not? Default: TRUE |
x |
nem object |
... |
other arguments to pass |
moduleNetwork
is an alternative to exhaustive search
by the function score
and more accurate than pairwise.posterior
and triples.posterior
.
It uses clustering to sucessively split the network into smaller modules, which can then be estimated completely. Connections between modules are estimated by performing a constraint greedy hillclimbing.
graph |
the inferred directed graph (graphNEL object) |
mLL |
marginal likelihood of final model |
pos |
posterior over effect positions |
mappos |
MAP estimate of effect positions |
type |
as used in function call |
para |
as used in function call |
hyperpara |
as used in function call |
lambda |
as in function call |
selected |
selected E-gene subset |
Holger Froehlich
data("BoutrosRNAi2002") res <- moduleNetwork(BoutrosRNAiDiscrete[,9:16],para=c(.13,.05)) # plot graph plot(res,what="graph") # plot posterior over effect positions plot(res,what="pos") # estimate of effect positions res$mappos