compare_expected_vs_observed: Compare the observed frequencies of combinations with their...

In RareComb: Combinatorial and Statistical Analyses of Rare Events

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')

RareComb documentation built on March 18, 2022, 7:02 p.m.