pairwise.posterior {nem} | R Documentation |
Function pairwise.posterior
estimates the hierarchy edge by edge. In each step only a pair of nodes
is involved and no exhaustive enumeration of model space is needed as in function score
.
pairwise.posterior(D, type = "mLL", para = NULL, hyperpara = NULL, Pe = NULL, Pmlocal = NULL, Pm = NULL, lambda = 0, delta=1, verbose = TRUE) ## S3 method for class 'pairwise': print(x,...)
D |
data matrix. Columns correspond to the nodes in the silencing scheme. Rows are phenotypes. |
type |
see nem |
para |
vector with parameters a and b for "mLL", if count matrices are used |
hyperpara |
vector with hyperparameters a0, b0, a1, b1 for "FULLmLL" |
Pe |
prior position of effect reporters. Default: uniform over nodes in hierarchy |
Pmlocal |
local model prior for the four models tested at each node: a vector of length 4 with positive entries summing to one |
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) |
verbose |
do you want to see progress statements printed or not? Default: TRUE |
x |
nem object |
... |
other arguments to pass |
pairwise.posterior
is a fast(er) heuristic alternative to exhaustive search
by the function score
. For each pair (A
,B
) of perturbed genes
it chooses between four possible models: A..B
(unconnected), A->B
(superset),
A<-B
(subset), or A<->B
(indistinguishable).
The result is the graph built from the maximum aposteriori models for each edge.
print.pairwise
gives an overview over the 'pairwise' object.
nem object
Florian Markowetz <URL: http://genomics.princeton.edu/~florian>
data("BoutrosRNAi2002") res <- nem(BoutrosRNAiDiscrete[,9:16],para=c(.13,.05),inference="pairwise") # plot graph plot(res,what="graph") # plot posterior over effect positions plot(res,what="pos") # estimate of effect positions res$mappos