Functional test enrichment functions about hmvar HOT 2 CLOSED

There are now two major functions (and associated utility functions):

1. test_go which uses topGO to perform different enrichment analysis. It can perform any test supported by topGO, including methods that control for the GO topology, and returns both topGOdata and topGOresult objects. Its main limitation is that it only can handle Gene Ontology annotations.

2. gsea performs Gene-set enrichment analysis via either a Wilcoxon rank sum test, or a Kolmogorov-Smirnov test. The main advantage is that it doesn't require arbitrary threshold values to determine significance, and it can work with any arbitrary annotation. The main disadvantage is that it cannot incorporate information about the topology of the annotation.

from hmvar.

Created a third function

3. sign_test performs sign_test to identify potential selection. It uses a score associated with genes and determines if the number of positive scores for a group of genes that share an annotation term is greater than expected by chance given the background level of positive and negative scores. It uses a binomial probability to calculate a p-value. Makes very few assumptions and it is a special case of Orr's sign_test.

from hmvar.