Description Usage Arguments Details Value Author(s) References See Also Examples
Performs posterior inference on the output of the main function
1 | Inference(listComplete, G, M, niter, burnin, threshold = 0.5)
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listComplete |
Output of the main function |
G |
Number of gene expression probes |
M |
Number of CGH probes |
niter |
Number of Monte Carlo Markov Chain iterations |
burnin |
Burn-in |
threshold |
Threshold on the posterior probabilities of inclusion of the association matrix |
Wrapper function which calls InferenceR, InferenceXi, InferenceA, InferenceMu, InferenceSd on the output of the main function.
A list made by the following items
R |
Binary matrix of estimated association |
Xi |
Matrix of estimated copy number states |
A |
Estimated transition matrix |
Mu |
Estimated vector of state specific means |
Sd |
Estimated vector of state specific standard deviations |
Alberto Cassese
Cassese A, Guindani M, Tadesse M, Falciani F, Vannucci M. A hierarchical Bayesian model for inference of copy number variants and their association to gene expression. Annals of Applied Statistics, 8(1), 148-175.
Cassese A, Guindani M, Vannucci M. A Bayesian integrative model for genetical genomics with spatially informed variable selection. Cancer Informatics.
See Also InferenceR
,InferenceXi
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ## Not run:
data(NCI_60)
Y <- NCI_60$Affy
X <- NCI_60$aCGH
distance <- NCI_60$distance
disfix <- 146274826
xi <- InitXi(X)
tran <- Tran(xi)
mu <- InitMu()
d=0.2587288
Y <- Center(Y)
res <- iBAT(Y=Y,X=X,distance=distance,disfix=disfix,xi=xi,tran=tran,mu=mu,d=d)
summRes <- Inference(res,G=dim(Y)[[2]],M=dim(X)[[2]],niter=niter,burnin=bi,threshold=0.5)
## End(Not run)
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