stat_test_SMC: Apply statistical tests to a stratification (SMC)

Description Usage Arguments Value See Also Examples

View source: R/SMC.R

Description

stat_test_SMC tests for enrichment or depletion in the different strata of a stratification of the mutational catalogue for every signature independently by applying Kruskal Wallis tests. For those signatures where the Kruskal Wallis test gives a significant p-value, pairwise posthoc tests are carried out by calling posthoc.kruskal.nemenyi.test. Additionally all data is tested for normality by Shapiro Wilk tests, so that the user may apply ANOVA and pairwise posthoc t-test where allowed.

Usage

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stat_test_SMC(in_strat_list, in_flag = "norm")

Arguments

in_strat_list

A list with entries exposures_list, catalogues_list, cohort and name_list as in the output of run_SMC.

  • exposures_list: The list of s strata specific exposures Hi, all are numerical data frames with l rows and m columns, l being the number of signatures and m being the number of samples

  • catalogues_list: A list of s strata specific cohortwide (i.e. averaged over cohort) normalized exposures

  • cohort: subgroups_df adjusted for plotting

  • name_list: Names of the contructed strata.

in_flag

If "norm", all tests are performed on normalized exposures, otherwise the absolute exposures are taken.

Value

A list with entries kruskal_df, shapiro_df, kruskal_posthoc_list,

See Also

run_SMC

posthoc.kruskal.nemenyi.test

kruskal.test

shapiro_if_possible

shapiro.test

Examples

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