SimuData: Simulate two sequences of p-values by accounting for the...

In ReAD: Powerful Replicability Analysis of Genome-Wide Association Studies

Simulate two sequences of p-values by accounting for the local dependence structure via a hidden Markov model.

Description

Simulate two sequences of p-values by accounting for the local dependence structure via a hidden Markov model.

Usage

SimuData(
  J = 10000,
  pi = c(0.25, 0.25, 0.25, 0.25),
  A = 0.6 * diag(4) + 0.1,
  muA = 2,
  muB = 2,
  sdA = 1,
  sdB = 1
)

Arguments

J	The number of features to be tested in two studies.
pi	The stationary probabilities of four hidden joint states.
A	The 4-by-4 transition matrix.
muA	Mean of the normal distribution generating the p-value in study 1.
muB	Mean of the normal distribution generating the p-value in study 2.
sdA	The standard deviation of the normal distribution generating the p-value in study 1.
sdB	The standard deviation of the normal distribution generating the p-value in study 2.

Value

A list:

pa	A numeric vector of p-values from study 1.
pb	A numeric vector of p-values from study 2.
theta1	The true states of features in study 1.
theta2	The true states of features in study 2.

ReAD documentation built on July 9, 2023, 6:38 p.m.