cobiclust (version 0.1.0)

cobiclust: Perform a biclustering adapted to overdispersed count data.

Description

Perform a biclustering adapted to overdispersed count data.

Usage

cobiclust(x, K = 2, G = 3, nu_j = NULL, a = NULL, akg = FALSE,
  cvg_lim = 1e-05, nbiter = 5000)

Value

An object of class cobiclustering

Arguments

x

the input matrix of observed data.

K

an integer specifying the number of groups in rows.

G

an integer specifying the number of groups in columns.

nu_j

a vector of . The length is equal to the number of colums.

a

an numeric.

akg

a logical variable indicating whether to use a common dispersion parameter (akg = FALSE) or a dispersion parameter per cocluster (akg = TRUE).

cvg_lim

a number specifying the threshold used for convergence criterion (cvg_lim = 1e-05 by default).

nbiter

the maximal number of iterations for the global loop of variational EM algorithm (nbiter = 5000 by default).

See Also

cobiclustering for the cobiclustering class.

Examples

npc <- c(50, 40) # nodes per class
KG <- c(2, 3) # classes
nm <- npc * KG # nodes
Z <- diag( KG[1]) %x% matrix(1, npc[1], 1)
W <- diag(KG[2]) %x% matrix(1, npc[2], 1)
L <- 70 * matrix( runif( KG[1] * KG[2]), KG[1], KG[2])
M_in_expectation <- Z %*% L %*% t(W)
size <- 50
M<-matrix(
 rnbinom(
   n = length(as.vector(M_in_expectation)),
   mu = as.vector(M_in_expectation), size = size)
 , nm[1], nm[2])
rownames(M) <- paste("OTU", 1:nrow(M), sep = "_")
colnames(M) <- paste("S", 1:ncol(M), sep = "_")
res <- cobiclust(M, K = 2, G = 3, nu_j = rep(1,120), a = 1/size, cvg_lim = 1e-5)