Identify Prognosis-Related Pathways Altered by Somatic Mutation
c(person(given = "Junwei", family = "Han", email = "hanjunwei1981@163.com", role  = c("aut", "cre", "cph")),
person(given = "Yalan", family = "He", role  = "aut"),person(given = "Xiangmei", family = "Li", role  = "aut"))
We innovatively defined a pathway mutation accumulate perturbation score (PMAPscore) to reflect the position and the cumulative effect of the genetic mutations at the pathway level. Based on the PMAPscore of pathways, identified prognosis-related pathways altered by somatic mutation and predict immunotherapy efficacy by constructing a multiple-pathway-based risk model (Tarca, Adi Laurentiu et al (2008) <doi:10.1093/bioinformatics/btn577>).
base, clusterProfiler, glmnet, graphics, grDevices, maftools,
org.Hs.eg.db, pROC, stats, survival, survminer, utils
Junwei Han [aut, cre, cph],
Yalan He [aut],
Xiangmei Li [aut]

Calculate Pairwise Multiple Comparisons of Mean Rank Sums.
The Kruskal and Wallis one-way analysis of variance by ranks
can be employed, if the data do not meet the assumptions
for one-way ANOVA. Provided that significant differences
were detected by the Kruskal-Wallis-Test, one may be interested
in applying post-hoc tests for pairwise multiple comparisons
of the ranked data. Similarly, one-way ANOVA with repeated
measures that is also referred to as ANOVA with unreplicated
block design can also be conducted via the Friedman-Test.
The consequent post-hoc pairwise multiple comparison test according
to Nemenyi is also provided in this package.

Calculate Pairwise Multiple Comparisons of Mean Rank Sums

The Kruskal and Wallis one-way analysis of variance by ranks
can be employed, if the data do not meet the assumptions
for one-way ANOVA. Provided that significant differences
were detected by the Kruskal-Wallis-Test, one may be interested
in applying post-hoc tests for pairwise multiple comparisons
of the ranked data (Nemenyi's test, Dunn's test, Conover's test,
van der Waerden's test). Similarly, one-way ANOVA with repeated
measures that is also referred to as ANOVA with unreplicated
block design can also be conducted via the Friedman-Test.
The consequent post-hoc pairwise multiple comparison tests according
to Nemenyi and Conover are also provided in this package.