stat_test_SMC: Apply statistical tests to a stratification (SMC)
In YAPSA: Yet Another Package for Signature Analysis
Description
Usage
Arguments
Value
See Also
Examples
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
1
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
posthoc.kruskal.nemenyi.test).
See Also
Examples
1
YAPSA documentation built on Nov. 8, 2020, 4:59 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value See Also Examples
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
1 | stat_test_SMC(in_strat_list, in_flag = "norm")
|
Arguments
in_strat_list |
A list with entries
|
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 byposthoc.kruskal.nemenyi.test).
See Also
Examples
1 |
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.