GeneWalk synthetic data params

Usage

params_genewalk_data(
  n_signal_genes = 150L,
  n_noise_genes = 150L,
  n_roots = 10L,
  depth = 3L,
  branching = 3L,
  p_lateral = 0.1,
  p_ppi = 0.05,
  min_annotations = 10L,
  max_annotations = 25L,
  min_noise_subtrees = 15L
)

Arguments

n_signal_genes: Integer. Number of signal genes. Defaults to 150L.
n_noise_genes: Integer. Number of noise genes. Defaults to 150L.
n_roots: Integer. Number of ontology root nodes. Defaults to 10L.
depth: Integer. Depth of each ontology subtree. Defaults to 3L.
branching: Integer. Base branching factor per ontology node. Defaults to 3L.
p_lateral: Numeric. Probability of a lateral edge between sibling nodes. Defaults to 0.1.
p_ppi: Numeric. Probability of a PPI edge between any two genes in the same group. Defaults to 0.05.
min_annotations: Integer. Minimum ontology term annotations per gene. Defaults to 10L.
max_annotations: Integer. Maximum ontology term annotations per gene. Defaults to 25L.
min_noise_subtrees: Integer. Minimum distinct ontology subtrees a noise gene must span. Defaults to 15L.

Value

A named list with the following elements:

n_signal_genes - Integer. Number of signal genes. Defaults to 150L.
n_noise_genes - Integer. Number of noise genes. Defaults to 150L.
n_roots - Integer. Number of ontology root nodes. Defaults to 10L.
depth - Integer. Depth of each ontology subtree. Defaults to 3L.
branching - Integer. Base branching factor per ontology node. Defaults to 3L.
p_lateral - Numeric. Probability of a lateral edge between sibling nodes. Defaults to 0.1.
p_ppi - Numeric. Probability of a PPI edge between any two genes in the same group. Defaults to 0.05.
min_annotations - Integer. Minimum ontology term annotations per gene. Defaults to 10L.
max_annotations - Integer. Maximum ontology term annotations per gene. Defaults to 25L.
min_noise_subtrees - Integer. Minimum distinct ontology subtrees a noise gene must span. Defaults to 15L.