stat_test_SMC: Apply statistical tests to a stratification (SMC)
In eilslabs/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
2
eilslabs/YAPSA documentation built on May 16, 2019, 1:23 a.m.
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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 2 |
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