stat_test_SMC {YAPSA} | R Documentation

## Apply statistical tests to a stratification (SMC)

### 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 `kwAllPairsNemenyiTest`. 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

    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`,

- `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).

- `shapiro_df`: A data frame containing results (p values) of the Shapiro Wilk tests (tests for normal distribution 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 `kwAllPairsNemenyiTest`).

### See Also

`run_SMC`

`kwAllPairsNemenyiTest`

`kruskal.test`

`shapiro_if_possible`

`shapiro.test`

### Examples

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[Package YAPSA version 1.20.1 Index]