| score {nem} | R Documentation |
Function to compute the marginal likelihood of a set of phenotypic hierarchies.
score(models, D, type="mLL", para=NULL, hyperpara=NULL, Pe=NULL, Pm=NULL, lambda=0, verbose=TRUE) # S3 metehods for class 'score' print.score(x, ...)
models |
a list of adjacency matrices with unit main diagonal |
D |
data matrix. Columns correspond to the nodes in the silencing scheme. Rows are effect reporters. |
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 |
para |
Vector with parameters a and b (for "mLL" with count data) |
hyperpara |
Vector with hyperparameters a0, b0, a1, b1 for "FULLmLL" |
Pe |
prior position of effect reporters. Default: uniform over nodes in silencing scheme |
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. |
verbose |
output while running or not |
x |
nem object |
... |
other arguments to pass |
Scoring models by marginal log-likelihood is implemented in function
score. Input consists of models and data, the type of the score
("mLL" or "FULLmLL"), the corresponding paramters
(para) or hyperparameters (hyperpara), a prior for phenotype
positions (Pe) and model structures priorPhi with regularization parameter lambda.
score is usually called within function nem.
graph |
the model with highest marginal likelihood (graphNEL object) |
mLL |
vector of marginal likelihoods for all models |
pos |
a list of estimated positions of effect reporters for each model |
mappos |
a list of maximum aposteriori estimates of effect positions for each model |
type |
as used in function call |
para |
as used in function call |
hyperpara |
as used in function call |
lambda |
as in function call |
Florian Markowetz <URL: http://genomics.princeton.edu/~florian>
nem, mLL, FULLmLL, enumerate.models
# Drosophila RNAi and Microarray Data from Boutros et al, 2002
data("BoutrosRNAi2002")
D <- BoutrosRNAiDiscrete[,9:16]
# enumerate all possible models for 4 genes
models <- enumerate.models(unique(colnames(D)))
# score models with marginal likelihood
result <- score(models,D,type="mLL",para=c(.13,.05))
# plot graph
plot(result,what="graph")
# plot scores
plot(result,what="mLL")
# plot posterior of E-gene positions
plot(result,what="pos")
# MAP estimate of effect positions
result$mappos[[which.max(result$mLL)]]