Description Usage Arguments Value Author(s) See Also Examples
This function simulates MBASIC model with two states: background or binding. This mimics the standard ChIP-seq experiment.
1 2 | MBASIC.sim.binary(I, fac, J, f, struct = NULL, beta = 0.1, zeta = 0.1,
beta.non = 0.1, xi = 6, family = "lognormal")
|
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". |
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. |
Chandler Zuo zuo@stat.wisc.edu
1 | dat.sim <- MBASIC.sim.binary(I = 100, fac = rep(1:5, each = 2), J = 3, f = 5)
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