stat_test_subgroups: Test for differences in average signature exposures between...

In huebschm/YAPSA: Yet Another Package for Signature Analysis

Description

Apply Kruskal-Wallis tests to detect differences in the signature exposures between different subgroups. Uses split_exposures_by_subgroups. Algorithm analogous to stat_test_SMC.

Usage

stat_test_subgroups(in_exposures_df, in_subgroups_df,
  in_subgroups.field = "subgroup", in_PID.field = "PID")

Arguments

in_exposures_df	Numerical data frame of the exposures (i.e. contributions of the different signatures to the number of point mutations per PID)
in_subgroups_df	Data frame indicating which PID belongs to which subgroup
in_subgroups.field	Name indicating which column in in_subgroups_df contains the subgroup information
in_PID.field	Name indicating which column in in_subgroups_df contains the PID information

Value

A list with entries kruskal_df, kruskal_posthoc_list,

• kruskal_df: A data frame containing results (statistic and p values) of the Kruskal Wallis tests (tests for enrichment or depletion in the different strata for every signature independently).

• kruskal_posthoc_list: A list of results of pairwise posthoc tests carried out for those signatures where the Kruskal Wallis test yielded a significant p-value (carried out by posthoc.kruskal.nemenyi.test).

See Also

split_exposures_by_subgroups

stat_test_SMC

posthoc.kruskal.nemenyi.test

kruskal.test

Examples

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huebschm/YAPSA documentation built on May 17, 2019, 9:11 p.m.