getIncidence

A vector containing the list of 
        possible gene ids in the universe (or experiment).

universeIDs

A GeneSet object containing a set of genes of
        interest


    Calculates the incidence of a gene set in an experiment


Current gene set enrichment methods rely upon permutations
for inference.  These approaches are computationally expensive
and have minimum achievable p-values based on the number of
permutations, not on the actual observed statistics.  We have
derived three parametric approximations to the permutation
distributions of two gene set enrichment test statistics.  We
are able to reduce the computational burden and granularity
issues of permutation testing with our method, which is
implemented in this package. npGSEA calculates gene set
enrichment statistics and p-values without the computational
cost of permutations.  It is applicable in settings where one
or many gene sets are of interest.  There are also built-in
plotting functions to help users visualize results.

Jessica Larson

npGSEA

Permutation approximation methods for gene set enrichment
analysis (non-permutation GSEA)

getIncidence function

Calculates the incidence of a gene set in an experiment

getIncidence: Determines the incidence of a gene set in a list of genes.

Description

Usage

Arguments

Value

Details

References

Examples