boot.genie3: GEne Network Inference with Ensemble of trees (GENIE3) with...

In rlebron-bioinfo/gnlearn: Genetic Network Learning

Description

This function allows you to learn a directed graph from a dataset using the GENIE3 algorithm.

Usage

boot.genie3(
  df,
  tree.method = c("rf", "et"),
  K = "sqrt",
  n.trees = 1000,
  min.weight = 0.1,
  R = 200,
  m = NULL,
  threshold = 0.5,
  to = c("igraph", "adjacency", "edges", "graph", "bnlearn"),
  cluster = parallel::detectCores(),
  seed = sample(1:10^6, 1)
)

Arguments

df	Dataset.
tree.method	Random Forest ('rf') or Extra-Trees ('et'). Default: 'rf'
K	Number of candidate regulators that are randomly selected at each tree node for the best split determination. Default: 'sqrt' (square root of the number of genes)
n.trees	Number of trees that are grown per ensemble. Default: 1000
min.weight	Minimum absolute value considered in the adjacency matrix. Lower values will be replaced by zero. Default: 0.1
R	Number of bootstrap replicates (optional). Default: 200
m	Size of training set (optional). Default: nrow(df)/2
threshold	Minimum strength required for a coefficient to be included in the average adjacency matrix (optional). Default: 0.5
to	Output format ('adjacency', 'edges', 'graph', 'igraph', or 'bnlearn') (optional).
cluster	A cluster object from package parallel or the number of cores to be used (optional). Default: parallel::detectCores()
seed	Seed used for random selection. Default: NULL

Examples

obj <- boot.genie3(df)
avg.g <- obj$average
g.rep <- obj$replicates

rlebron-bioinfo/gnlearn documentation built on July 25, 2020, 12:38 p.m.