choosepath

The index of focus set that has the first largest number of true discovereis

startingindex

A list of focus level gene sets,or GO (Gene Ontology) terms

fsets

A non-negative integer vector, which are the number of true discovereis, the length of the vector is the same as the list of focus level sets

lowdv

The function aims to find out the focus set index for which the true discoveries is the most and all other focus sets that are disjoint with it .

Closed testing has been proved powerful for true discovery guarantee. The computation of closed testing is, however, quite burdensome. A general way to reduce computational complexity is to combine partial closed testings for some prespecified feature sets of interest. Partial closed testings are performed at Bonferroni-corrected alpha level to guarantee the lower bounds for the number of true discoveries in prespecified sets are simultaneously valid. For any post hoc chosen sets of interest, coherence property is used to get the lower bound. In this package, we implement closed testing with globaltest to calculate the lower bound for number of true discoveries, see Ningning Xu et.al (2021) <arXiv:2001.01541> for detailed description.

choosepath: A set of focus set index

Description

Usage

Arguments

Value