bbm_data_generate: bbm_data_generate

In DPBBM: Dirichlet Process Beta-Binomial Mixture

Description

This is to generate the simulation data based on Beta-bionomial mixture model

Usage

bbm_data_generate(S=3, G=50, K=3, prob=rep(1,times=3),
                              alpha_band=c(2,6),
                              beta_band=c(2,6),
                              nb_mu=100,nb_size=0.2, plotf = FALSE, 
                              max_cor=0.5)

Arguments

S	Number of samples in the simulated data
G	Number of sites in the simulated data
K	Number of clusters that exist in the simulated data
prob	the cluster weight for each cluster
alpha_band	the region used to generate the parameter of beta distribution alpha
beta_band	the region used to generate the parameter of beta distribution beta
nb_mu	alternative parametrization via mean for Negative Binomial distribution
nb_size	target for number of successful trials, or dispersion parameter (the shape parameter of the gamma mixing distribution) for Negative binomial distrition. Must be strictly positive, need not be integer.
plotf	option for whether plot the generated data according to clusters or not
max_cor	The maximized correlation allowed for the simulated data, which used to guarantee the data is not highly correlated.

Details

The Dirichlet Process based beta-binomial mixture model clustering

Value

The function returns simulation data generated based on beta binomial mixture model

Author(s)

Lin Zhang, PhD <[e-mail]>

References

Reference coming soon!

Examples

set.seed(123455)
S <- 4
G <- 100
K <- 3
nb_mu <- 100
nb_size <- 0.8
prob <- c(1,1,1)
mat <- bbm_data_generate(S=S,G=G,K=K,prob=prob,alpha_band=c(2,6),beta_band=c(2,6),
                         nb_mu=nb_mu,nb_size=nb_size, plotf = TRUE, max_cor=0.5) 
table(mat$gamma)
pie(mat$gamma)
id <- order(mat$gamma);
c <- mat$gamma[id]
mat_ratio <- (mat$k+1)/(mat$n+1);
heatmap(mat_ratio[id,], Rowv = NA, Colv = NA, scale="none", RowSideColors=as.character(c), 
        xlab = "4 samples", ylab="100 RNA methylation sites")

DPBBM documentation built on May 1, 2019, 10:25 p.m.