binder: BINDER wrapper function.

In ptrcksn/BINDER: BayesIan gene regulatory Networks inferreD via gene coExpression and compaRative genomics

Description

BINDER wrapper function.

Usage

binder(proxy_regulon, expression, hyperparams = NULL, inits = NULL,
  O = NULL, delta_CM = "auto", delta_CP = "auto",
  is_coexpression = FALSE, model = "BINDER", n_chains = 1,
  n_draws = 1000, burn_in = 0, thin = 0, n_cores = 1, seed = 1)

Arguments

proxy_regulon	Data frame comprising columns: regulator, target_candidate, ortholog_module_status (1 if orthologous, 0 otherwise), ME (1 if high affinity for regulator motif, 0 otherwise) and PE (1 if orthologous interaction, 0 otherwise).
expression	Numerical expression matrix; can be expression matrix with genes represented on rows and experimental conditions represented on columns or symmetric gene-gene coexpression matrix.
hyperparams	A named list of user-defined hyperparameters (see ?BINDER::run_sampler_binder, ?BINDER::run_sampler_non_auxiliary and ?BINDER::run_sampler_deterministic).
inits	A named list of user-defined initial values to begin each MCMC chain (see ?BINDER::run_sampler_binder, ?BINDER::run_sampler_non_auxiliary and ?BINDER::run_sampler_deterministic).
O	Named list where each name is a target candidate and each element is a character vector comprising names of genes that should not be included in the computation of CM and CP for the corresponding target candidate name; by default only autocoexpression is excluded.
delta_CM	Numerical cutoff point for coexpression module for CM: any values above threshold are considered to form a coexpression module with target_candidate; defaults to "auto" which represents the 95th percentile of coexpression scores involving target_candidate.
delta_CP	Numerical cutoff point for coexpression module for CM: any values above threshold are considered to form a coexpression module with target_candidate; defaults to "auto" which represents the 95th percentile of coexpression scores involving target_candidate.
is_coexpression	logical; if TRUE, expression matrix is treated as symmetric coexpression matrix.
model	Indicates which model should be fit to the data: one of "BINDER", "non_auxiliary" or "deterministic".
n_chains	Number of MCMC chains to run; defaults to 1.
n_draws	Number of MCMC draws to run; defaults to 1000.
burn_in	Number of MCMC draws to discard from the beginning of each chain; defaults to 0.
thin	Number of MCMC draws to discard between each accepted MCMC draw for each chain; defaults to 0.
seed	Seed for random number generation; defaults to 1.

Value

A list containing the MCMC draws for each model parameter for each chain for each putative regulor in proxy_regulon.

ptrcksn/BINDER documentation built on Nov. 5, 2019, 1:56 a.m.