genSimDat: Generate Simulated Data

In eLNNpairedCov: Model-Based Gene Selection for Paired Data

Generate Simulated Data

Description

Generate a simulated dataset from a mixture of Bayesian hierarchical models with two covariates: age and sex.

Usage

genSimDat(G, n, psi, t_pi, m.age = 50, sd.age = 5, p.female = 0.5)

Arguments

G	integer. Number of probes.
n	integer. Number of samples.
psi	numeric. A vector of model hyper-parameters with elements \alpha_1, \beta_1, k_1, \eta_{1,intercept}, \eta_{1,age}, \eta_{1,sex}, \alpha_2, \beta_2, k_2, \eta_{2,intercept}, \eta_{2,age}, \eta_{2,sex}, \alpha_3, \beta_3, k_3, \eta_{3,intercept}, \eta_{3,age}, \eta_{3,sex}.
t_pi	numeric. A vector of mixture proportions: \pi_1 (proportion for probes over-expressed in cases); \pi_2 (proportion for probes under-expressed in cases).
m.age	numeric. mean age.
sd.age	numeric. standard deviation of age.
p.female	numeric. proportion of females.

Value

An ExpressionSet object.

Note

Age will be mean-centered and scaled so that it will have mean zero and variance one.

Author(s)

Yixin Zhang [e-mail], Wei Liu [e-mail], Weiliang Qiu [e-mail]

References

Zhang Y, Liu W, Qiu W. A model-based clustering via mixture of hierarchical models with covariate adjustment for detecting differentially expressed genes from paired design. BMC Bioinformatics 24, 423 (2023)

Examples

set.seed(1234567)

true.psi = c(2, 1, 0.8,
             0.1, -0.01, -0.1,
             2, 1, 0.8,
             -0.1, -0.01, -0.1,
             2, 1, 0.8,
             -0.01, -0.1)
names(true.psi)=c("alpha1", "beta1", "k1",
                  "eta1.intercept", "eta1.Age", "eta1.Sex",
                  "alpha2", "beta2", "k2",
                  "eta2.intercept", "eta2.Age", "eta2.Sex",
                  "alpha3", "beta3", "k3",
                  "eta3.Age", "eta3.Sex")
true.pi=c(0.1, 0.1)
names(true.pi)=c("pi.OE", "pi.UE")
par.true=c(true.pi, true.psi)

esDiff = genSimDat(G = 1000, 
	       n = 20, 
	       psi = true.psi, 
	       t_pi = true.pi, 
	       m.age = 0, # scaled age 
	       sd.age = 1, # scaled age
	       p.female = 0.5)

print(esDiff)

eLNNpairedCov documentation built on May 29, 2024, 3:16 a.m.