rSEA-package: Simultaneous Enrichment Analysis (SEA) of all possible...

In rSEA: Simultaneous Enrichment Analysis

Description

This package uses raw p-values of genomic features as input and evaluates any given list of feature-sets or pathways. For each set the adjusted p-value and TDP lower-bound are calculated. The type of test can be defined by arguments and can be refined as necessary. The p-values are corrected for every possible set of features, making the method flexible in choice of pathway list and test type. For more details see: Ebrahimpoor, M (2019) <doi:10.1093/bib/bbz074>

Details

The unified null hypothesis is tested using closed testing procedure and all-resolutions inference. It combines the self-contained and ompetitive approaches in one framework. In short, using p-values of the individual features as input, the package can provide an FWER-adjusted p-value along with a lower bound and a point estimate for the proportion of true discoveries per feature-set. The flexibility in revising the choice of feature-sets without inflating type-I error is the most important property of SEA.

Author(s)

Mitra Ebrahimpoor.

Maintainer: Mitra Ebrahimpoor<[e-mail]>

References

Mitra Ebrahimpoor, Pietro Spitali, Kristina Hettne, Roula Tsonaka, Jelle Goeman, Simultaneous Enrichment Analysis of all Possible Gene-sets: Unifying Self-Contained and Competitive Methods, Briefings in Bioinformatics,bbz074 https://doi.org/10.1093/bib/bbz074

rSEA documentation built on March 23, 2020, 5:09 p.m.