FacPad (version 3.0)

gibbs2: A Collapsed Gibbs Sampling Algorithm for the Inference of Sparse Bayesian Factor Models_version2

Description

In each iteration, the algorithm iteratively updates each entry in the binary matrix Z, loading matrix W and factor activity matrix X, as well as other model parameters.

Usage

gibbs2(matrixY, matrixL,eta0,eta1,alpha_tau = 1, 
beta_tau = 0.01, tau_sig = 1, max_iter = 10000, 
thin = 10, alpha_sigma = 0.7, beta_sigma = 0.3, file_name)

Arguments

matrixY

The input treatment response matrix. It has dimension G by J,where G is the number of probesets and J is the number of different treatments. The (g,j)-th entry represents the ratio of the expression of the g-th probeset after and before the j-th treatment.

matrixL

The binary probeset-pathway association matrix.It has dimension G by K. If the (g,k)-th entry has value 1, it indicates that the g-th probeset is involved in the k-th pathway; and the (g,k)-th entry takes value 0 if there is no association relationship.

eta0

The bernoulli probability of entries in matrix Z taking a non-zero value given that the corresponding entry in matrix L is zero

eta1

The bernoulli probability of entries in matrix Z taking the value zero given that the corresponding entry in matrix L is one

alpha_tau

The alpha parameter of Gamma distribution used for the simulation of noise, default value=1

beta_tau

The beta parameter of Gamma distribution used for the simulation of noise, default value=0.01

tau_sig

Pre-defined precision of each entry in the factor loadings matrixW, default value=0

max_iter

The number of iterations of the collaped Gibbs sampling algorithm, default=10000

thin

The number of iteration cycle for the record of Gibbs samples. For the convenience of storage, the result of the Gibbs sampling will be kept every other "thin" iterations to alliviate the auto-correlation problem between adjacent interations of the Gibbs sampling process

alpha_sigma

the alpha parameter for the Gamma prior for matrixW

beta_sigma

The beta parameter for the Gamma prior for matrixW

file_name

name of the file saving the result

Value

The algorithm will store the inferred binary indicator matrix Z, loading matrix W and factor activity matrix X (as well as tau_g if not pre-difined) in each thinned iteration and write them into .RData file with name defined by the user.

Examples

data(matrixY)
data(matrixL)
result<-gibbs2(matrixY,matrixL,eta0=0.2,eta1=0.2,
max_iter=50,thin=10,file_name="test_v2_50iter.RData")