simulation: Simulation used in our article [TODO reference].

In 3inar/pmadsim: Prsospective Microarray Simulation Model

Description

This method generates a data set with the parameters we used in [TODO].

Usage

simulation()

Arguments

n_case	number of cases to simulate
n_control	number of controls to simulate

Value

A list containing the following values

expression	Gene expression matrix of simulated fold change values. Observations in rows, genes in columns
differential	Vector describing which genes are truly differentially expressed. Zero indicates no DE, -1 indicates down-regulation, 1 indicates up-regulation.
followup	Followup time for each observation. A number in [0, 1].
status	Vector denoting case–control status for each observation.

References

[TODO ref our article]

See Also

pmadsim

Examples

d <- simulation()
differential <- d$differential
expression <- d$expression
followup <- d$followup
status <- d$status

diff <- which(differential != 0)

gene <- sample(diff, 1)
plot(followup, expression[, gene], col=status, pch=20, ylim=c(-1.5, 1.5))
abline(lm(expression[status=="case", gene]~followup[status=="case"]))
abline(lm(expression[status=="control", gene]~followup[status=="control"]), col="red")

3inar/pmadsim documentation built on May 21, 2019, 2:31 a.m.