PLIS - Multiplicity Control using Pooled LIS Statistic
A multiple testing procedure for testing several groups of
hypotheses is implemented. Linear dependency among the
hypotheses within the same group is modeled by using hidden
Markov Models. It is noted that a smaller p value does not
necessarily imply more significance due to the dependency. A
typical application is to analyze genome wide association
studies datasets, where SNPs from the same chromosome are
treated as a group and exhibit strong linear genomic
dependency. See Wei Z, Sun W, Wang K, Hakonarson H (2009)
<doi:10.1093/bioinformatics/btp476> for more details.