Man pages for ArnaudDroitLab/GenomicOperations
GenomicOperations
| collapse_regions | Collapses a list of genomic ranges into a single set of... |
| combined_regions-GenomicOverlaps-method | Returns the combined regions from a GenomicOverlaps object. |
| combined_regions-set-GenomicOverlaps-GRanges-method | Set the combined regions from a GenomicOverlaps object. |
| consensus_indices | Determines which regions form a "consensus" from all input... |
| consensus_regions | Determines which regions form a "consensus" from all input... |
| coverage_df | Returns a data-frame giving the coverages for all elements of... |
| coverage_plot | Plots the coverages for all elements of a GenomicEnrichment... |
| enrichment_df | Returns a data-frame giving the enrichments for all elements... |
| enrichment_plot | Plots the enrichments for all elements of a GenomicEnrichment... |
| GenomicEnrichment | Performs region enrichment on a set of regions and returns... |
| GenomicEnrichment-class | GenomicEnrichment objects represent the enrichment of a set... |
| GenomicOverlaps | Create a GenomicOverlaps object. |
| GenomicOverlaps-class | GenomicOverlaps objects represent the overlaps of multiple... |
| initial_regions-GenomicOverlaps-method | Returns the initial regions from a GenomicOverlaps object. |
| intersect_indices | Calculate the intersection of a set of elements within a... |
| intersect_matrix | Returns the intersection matrix from a GenomicOverlaps... |
| intersect_regions | Calculate the intersection of a set of elements within a... |
| length-GenomicEnrichment-method | Returns the number of elements of a GenomicEnrichment object. |
| length-GenomicOverlaps-method | Returns the number of elements of a GenomicOverlaps object. |
| names-GenomicEnrichment-method | Returns the names of the elements of a GenomicEnrichment... |
| names-GenomicOverlaps-method | Returns the names of the elements of a GenomicOverlaps... |
| names-set-GenomicEnrichment-character-method | Set names of the elements of a GenomicEnrichment object. |
| names-set-GenomicOverlaps-character-method | Set names of the elements of a GenomicOverlaps object. |
| pairwise_overlap | Calculate the pairwise overlaps of all factors within a... |
| plot_venn | Generates a venn diagram from a GenomicOverlaps object. |
| project_ranges | Projects the ranges in query into the ranges in target. |
| proportion_df | Returns a data-frame giving the coverage proportions for all... |
| proportion_plot | Plots the coverage proportions for all elements of a... |
| single_region_enrichment | Calculates enrichment ratios for query regions against a... |
| union_indices | Calculate the union of a set of elements within a... |
| union_regions | Calculate the union of a set of elements within a... |
