Enrichment Tool

Example usage of EnrichmentTool class

First select studies to use:

In [1]: from DAE import vDB

In [2]: studies = vDB.get_studies('ALL WHOLE EXOME')

In [3]: denovo_studies = [st for st in studies if 'WE' ==

In [4]: autism_studies = [st for st in denovo_studies if 'autism' ==

Then create a background model object:

In [5]: from enrichment_tool.background import SamochaBackground

In [6]: background = SamochaBackground()

After that create a counter object:

In [7]: from enrichment_tool.event_counters import GeneEventsCounter

In [8]: counter = GeneEventsCounter()

Create an enrichment tool:

In [9]: from enrichment_tool.tool import EnrichmentTool

In [10]: tool = EnrichmentTool(background, counter)

Select a gene set to work with:

In [11]: from DAE import get_gene_sets_symNS

In [12]: gt = get_gene_sets_symNS('main')

In [13]: gene_set = gt.t2G['chromatin modifiers'].keys()

And then we are ready to perform the actual calculations:

In [14]: res = tool.calc(autism_studies, 'prb', 'LGDs', gene_set)

The result is a dictionary. The keys in the dictionary are:

In [16]: res.keys()
Out[16]: ['rec', 'all', 'male', 'female']

Each value in the dictionary is an instance of the class EnrichmentResult:

In [19]: r = res['rec']

In [20]: len(r.events)
Out[20]: 39

In [21]: len(r.overlapped)
Out[21]: 9

In [22]: r.expected
Out[22]: 0.8992414922169882

In [23]: r.pvalue
Out[23]: 9.4660348870512223e-07

Classes and Functions