MBASIC.sim.binary: Simulate data for the MBASIC model with binary states.

In chandlerzuo/mbasic: Matrix Based Analysis for State-space Inference and Clustering.

Description

This function simulates MBASIC model with two states: background or binding. This mimics the standard ChIP-seq experiment.

Usage

MBASIC.sim.binary(I, fac, J, f, struct = NULL, beta = 0.1, zeta = 0.1,
  beta.non = 0.1, xi = 6, family = "lognormal")

Arguments

I	An integer for the total number of units.
fac	A vector of length N denoting the experimental condition for each replicate.
J	An integer for the number of clusters.
f	Numeric value for the target fold change. Default: 5. See MBASIC.sim for more information.
struct	An K by J integer matrix. The j-th column denotes the levels for the cluster level parameter. See details for more information. Default: NULL.
beta	Hyper parameter for simulating the entries of the W matrix. Each entry in the W matrix follows distribution Beta(beta, beta). Default: 0.1.
zeta	The probability that each unit does not belong to any cluster. Default: 0.1.
beta.non	The hyper parameter for simulating the probability for unclustered units. Default: 0.1.
xi	Parameter for the magnitude of each observations. Default: 6. See MBASIC.sim for more information.
family	A parameter for the family of distribution to be used. Either "lognormal" or "negbin". Default: "lognormal".

Value

A list containing:

Mu0	An N by I matrix. The (n,i)-th entry is the mean of the control experiment for the n-th experiment at unit i.
Y	A matrix where each row is the counts for each replicates at all loci.
W	A K by J matrix. Each row is the indicators of the loci sets related an individual replicate.
Z	An I by J matrix. Each column is the indicator for an individual loci set.
Theta	A K by I matrix. The (k,i)-th element is the indicator of whether the i-th unit is binding for condition k.
pi	A vector of length J. The j-th entry is the prior probability for each loci to belong to the j-th cluster.
non.id	A vector of length I indicating the number of each column not to belong to any cluster.
fac	A vector of length N denoting the experimental condition for each replicate.
bkng	Mean value of the responses with background state.
snr	The ratio between the mean value of the responses with the binding state and the background state.

Author(s)

Chandler Zuo [e-mail]

See Also

MBASIC.sim

Examples

dat.sim <- MBASIC.sim.binary(I = 100, fac = rep(1:5, each = 2), J = 3, f = 5)

chandlerzuo/mbasic documentation built on May 13, 2019, 3:24 p.m.