extend_solutions: Extend a solutions data frame to include outcome evaluations

In metasnf: Meta Clustering with Similarity Network Fusion

Extend a solutions data frame to include outcome evaluations

Description

Extend a solutions data frame to include outcome evaluations

Usage

extend_solutions(
  sol_df,
  target_dl = NULL,
  dl = NULL,
  cat_test = "chi_squared",
  min_pval = 1e-10,
  processes = 1,
  verbose = FALSE
)

Arguments

sol_df	Result of batch_snf storing cluster solutions and the settings that were used to generate them.
target_dl	A data list with features to calculate p-values for. Features in the target list will be included during p-value summary measure calculations.
dl	A data list with features to calcualte p-values for, but that should not be incorporated into p-value summary measure columns (i.e., min/mean/max p-value columns).
cat_test	String indicating which statistical test will be used to associate cluster with a categorical feature. Options are "chi_squared" for the Chi-squared test and "fisher_exact" for Fisher's exact test.
min_pval	If assigned a value, any p-value less than this will be replaced with this value.
processes	The number of processes to use for parallelization. Progress is only reported for sequential processing (processes = 1).
verbose	If TRUE, output progress to console.

Value

An extended solutions data frame (ext_sol_df class object) that contains p-value columns for each outcome in the provided data lists

Examples

input_dl <- data_list(
    list(gender_df, "gender", "demographics", "categorical"),
    list(diagnosis_df, "diagnosis", "clinical", "categorical"),
    uid = "patient_id"
)

sc <- snf_config(input_dl, n_solutions = 2)

sol_df <- batch_snf(input_dl, sc)

ext_sol_df <- extend_solutions(sol_df, input_dl)

metasnf documentation built on April 3, 2025, 5:40 p.m.