compare_expected_vs_observed {RareComb}

Compare the observed frequencies of combinations with their expected frequencies under the assumption of independence within a single group

Description

This function takes a Boolean dataframe as input and compares the observed frequency of combinations that meet the criteria specified by the users with their corresponding expectation derived under the assumption of independence between the constituent elements of each combination

Usage

compare_expected_vs_observed(boolean_input_df, combo_length, min_indv_threshold,
                             max_freq_threshold, input_format,
                             pval_filter_threshold, adj_pval_type)

Arguments

boolean_input_df

An input Boolean dataframe with multiple input variables

combo_length

The length of the combinations specified by the user

min_indv_threshold

Minimum number of instances that support the combination

max_freq_threshold

Maximum fraction of the cohort size that could support a combination (i.e., filter out highly frequent events)

input_format

Optional | Naming convention used for input variables (Default = 'Input_')

pval_filter_threshold

Optional | p-value cut-off to use for multiple testing adjustment (Default = 0.05)

adj_pval_type

Optional | Type of multiple testing corrections to use (Default = 'BH'; Alternative option = 'bonferroni')

Value

A dataframe with the list of multiple-testing adjusted statistically significant combinations along with quantitative measures (frequencies, p-values etc) that support the findings.

Author(s)

Vijay Kumar Pounraja

Examples

   compare_expected_vs_observed(boolean_input_df, 2, 10, 0.25, 0.05,
                                input_format = 'Input_', adj_pval_type = 'BH')