Enrichments

An important endgame step in 5C analysis is the quantification of overlap between specific interaction classes and traditional genomic annotations. lib5c provides a system for performing such an enrichment analysis.

Command-line interface

To plot traditional enrichments, run

$ lib5c plot enrichment

To plot the enrichment of occupied motifs with a specific orientation, run

$ lib5c plot convergency

Exposed functionality

The exposed functions for computing enrichments are:

• lib5c.algorithms.enrichment.count_intersections_all()

• lib5c.algorithms.enrichment.get_annotation_percentage_all()

• lib5c.algorithms.enrichment.get_fold_change_all()

• lib5c.algorithms.enrichment.get_fisher_exact_pvalue_all()

• lib5c.algorithms.convergency.compute_convergency()

The exposed functions for visualization are:

• lib5c.plotters.enrichment.plot_looptype_vs_annotation_heatmap()

• lib5c.plotters.enrichment.plot_annotation_vs_annotation_heatmap()

• lib5c.plotters.enrichment.plot_stack_bargraph()

• lib5c.plotters.convergency.plot_convergency()