Description Usage Arguments See Also
View source: R/sim_pants_mediation.R
Simulate pants
with mediation to estimate size (effect=0) & power (effect>0).
1 2 3 | 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)
|
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 |
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 |
seed |
Random seed. |
verbose |
Logical; should the number of simulations be printed every 100 simulations? |
ker |
Laplacian kernel matrix representing the interaction network. |
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