sim_pants_mediation: Simulate 'pants' with mediation to estimate size & power

Description Usage Arguments See Also

View source: R/sim_pants_mediation.R

Description

Simulate pants with mediation to estimate size (effect=0) & power (effect>0).

Usage

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sim_pants_mediation(Gmat, exposure, effect.v = c(0, 0.2), alpha = 0.05,
  nsim = 10^3, nperm = 10^3, ncores = 1, seed = 1,
  verbose = TRUE, ker = NULL)

Arguments

Gmat

Binary feature (e.g. gene) by pathway inclusion matrix, indicating which features are in which pathways.

exposure

Numeric vector or matrix of exposures. Ignored if type!="mediation".

effect.v

Numeric vector of log fold-changes or percent of phentotypes to add.

alpha

Alpha level.

nsim

Number of simulations.

nperm

Number of sample permutations to evaluate significance of pathways.

ncores

Integer. If > 1, number of cores to use for parallel computing. You can detect how many are available for your system using detectCores.

seed

Random seed.

verbose

Logical; should the number of simulations be printed every 100 simulations?

ker

Laplacian kernel matrix representing the interaction network.

See Also

sim_pants


jdreyf/PANTS documentation built on July 18, 2019, 10:12 a.m.