Man pages for SimonLarsen/higana
Ontology-based analysis of genetic variants.
| annotate | Annotate ontology with gene annotations. |
| collapse_redundant_terms | Collapse terms whose annotations are redundant with respect... |
| collapse_terms | Collapse a set of terms, rerouting their children directly to... |
| compute_gene_pcs | Compute principal components of SNPs annotated to genes. |
| compute_redundancy | Compute redundancy score for each term. |
| compute_term_pcs | Compute principal components of SNPs annotated to ontology... |
| compute_term_pcs_stepdown | Compute principal components of ontology terms for stepdown... |
| extract_pcs | Extract the PCs of a specific set of terms. |
| filter | Filter ontology to a specific set of terms. |
| filter_obsolete | Removes obsolete terms from the ontology. |
| filter_unannotated | Removes unannotated terms from the ontology. |
| permute | Permute an ontology. |
| plot_hierarchy | Plot part of an ontology as a tree. |
| propagate_annotations | Propagates annotations up through the hierarchy. |
| read_bed | Open PLINK .bed file and create gene mapping. |
| read_gaf | Read annotations from GAF file. |
| read_obo | Read ontology from OBO file. |
| recompute_ancestors | Recomputes 'ancestors' field for each term. |
| test_genes | Perform association test for genes. |
| test_terms | Perform association test for terms. |
| unite_roots | Unites a set of roots in the ontology under a common root. |
