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Wrapper function to generate CoReMo parameters

params_coremo.Rd

Wrapper function to generate CoReMo parameters

Usage

params_coremo(
  epsilon = 2,
  k_min = 2L,
  k_max = 150L,
  min_size = NULL,
  junk_module_threshold = 0.05,
  rbf_func = c("gaussian", "inverse_quadratic", "bump"),
  cor_method = c("spearman", "pearson")
)

Arguments

epsilon

Numeric. Epsilon parameter for the chosen RBF function, see rbf_func. The higher, the more aggressively low correlations will be shrunk. Defaults to 2.0.

k_min

Integer. Minimum and maximum number of cuts to use for the hierarchical clustering. Defaults to 2L.

k_max

Integer. Minimum and maximum number of cuts to use for the hierarchical clustering. Defaults to 150L.

min_size

Integer or NULL. Minimum size of the clusters. Smaller clusters will be combined together. Defaults to NULL.

junk_module_threshold

Numeric. Threshold for the minimum correlation to be observed in a module. Defaults to 0.05.

rbf_func

String. Type of RBF you wish to apply to down-weigh weak correlations. One of c("gaussian", "inverse_quadratic", "bump"). Defaults to "gaussian".

cor_method

String. The type of correlation to use. One of c("spearman", "pearson"). Defaults to "spearman".

Value

A named list with the following elements:

  • epsilon - Numeric. Epsilon parameter for the chosen RBF function, see rbf_func. The higher, the more aggressively low correlations will be shrunk. Defaults to 2.0.

  • k_min - Integer. Minimum and maximum number of cuts to use for the hierarchical clustering. Defaults to 2L.

  • k_max - Integer. Minimum and maximum number of cuts to use for the hierarchical clustering. Defaults to 150L.

  • min_size - Integer or NULL. Minimum size of the clusters. Smaller clusters will be combined together. Defaults to NULL.

  • junk_module_threshold - Numeric. Threshold for the minimum correlation to be observed in a module. Defaults to 0.05.

  • rbf_func - String. Type of RBF you wish to apply to down-weigh weak correlations. One of c("gaussian", "inverse_quadratic", "bump"). Defaults to "gaussian".

  • cor_method - String. The type of correlation to use. One of c("spearman", "pearson"). Defaults to "spearman".