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| GenomicInteractions-package | A package for looking at genomic interaction data. |
| $-method | Quick access to GenomicInteractions metadata columns |
| $<--method | Quick access to GenomicInteractions metadata columns |
| anchorOne | Functions to access data held in a GenomicInteractions object. |
| anchorOne-method | Functions to access data held in a GenomicInteractions object. |
| anchorTwo | Functions to access data held in a GenomicInteractions object. |
| anchorTwo-method | Functions to access data held in a GenomicInteractions object. |
| annotateAnchors | Annotate anchors |
| annotateAnchors-method | Annotate anchors |
| annotateInteractions | Annotate the interactions in a GenomicInteractions object |
| annotateInteractions-method | Annotate the interactions in a GenomicInteractions object |
| annotationFeatures | Functions to access data held in a GenomicInteractions object. |
| annotationFeatures-method | Functions to access data held in a GenomicInteractions object. |
| c | Combine GenomicInteractions Methods |
| c-method | Combine GenomicInteractions Methods |
| calculateDistances | Calculate interaction distances |
| calculateDistances-method | Calculate interaction distances |
| capitalize | Capitalize first letter of string |
| categoriseInteractions | Get the numbers of interaction types existing in your data |
| countOverlaps-method | Find overlaps between GRanges and GenomicInteractions objects |
| countsBetweenAnchors | Summarise Interactions between defined anchors |
| countsBetweenAnchors-method | Summarise Interactions between defined anchors |
| description | Functions to access data held in a GenomicInteractions object. |
| description-method | Functions to access data held in a GenomicInteractions object. |
| description<- | Functions to set data held in a GenomicInteractions object. |
| description<--method | Functions to set data held in a GenomicInteractions object. |
| export.bed12 | Export interactions in BED12 format. |
| export.bed12-method | Export interactions in BED12 format. |
| export.bedpe | Export interactions in BED Paired-End format. |
| export.bedpe-method | Export interactions in BED Paired-End format. |
| export.chiasig | Export interactions in a BEDPE-like format for use with ChiaSig |
| export.chiasig-method | Export interactions in a BEDPE-like format for use with ChiaSig |
| export.igraph | Export interactions to an igraph object. |
| export.igraph-method | Export interactions to an igraph object. |
| findOverlaps | Find overlaps between GRanges and GenomicInteractions objects |
| findOverlaps-method | Find overlaps between GRanges and GenomicInteractions objects |
| GenomicInteractions | Function to create a GenomicInteraction object |
| GenomicInteractions-class | A S4 class to represent interactions between genomic regions. |
| getters | Functions to access data held in a GenomicInteractions object. |
| get_binom_ligation_threshold | get self ligation threshold with binomial test |
| get_self_ligation_threshold | Get self ligation threshold with SD method from Heidari et al |
| hg19.refseq.transcripts | Human Refseq transcripts from chr 17-18 |
| hic_example_data | Example HiC dataset |
| interactionCounts | Functions to access data held in a GenomicInteractions object. |
| interactionCounts-method | Functions to access data held in a GenomicInteractions object. |
| interactionCounts<- | Functions to set data held in a GenomicInteractions object. |
| interactionCounts<--method | Functions to set data held in a GenomicInteractions object. |
| InteractionHelpers | Interaction Type Helpers |
| is.cis | Interaction Type Helpers |
| is.cis-method | Interaction Type Helpers |
| is.dd | Interaction Type Helpers |
| is.dd-method | Interaction Type Helpers |
| is.dt | Interaction Type Helpers |
| is.dt-method | Interaction Type Helpers |
| is.pd | Interaction Type Helpers |
| is.pd-method | Interaction Type Helpers |
| is.pp | Interaction Type Helpers |
| is.pp-method | Interaction Type Helpers |
| is.pt | Interaction Type Helpers |
| is.pt-method | Interaction Type Helpers |
| is.trans | Interaction Type Helpers |
| is.trans-method | Interaction Type Helpers |
| is.tt | Interaction Type Helpers |
| is.tt-method | Interaction Type Helpers |
| isInteractionType | Interaction Type Helpers |
| isInteractionType-method | Interaction Type Helpers |
| length-method | Get the length of a GenomicInteractions GIObject |
| makeGenomicInteractionsFromFile | Function to create GenomicInteraction objects from a file |
| mm9_refseq_promoters | Mouse Refseq promoters from chr 14-15 |
| name | Functions to access data held in a GenomicInteractions object. |
| name-method | Functions to access data held in a GenomicInteractions object. |
| name<- | Functions to set data held in a GenomicInteractions object. |
| name<--method | Functions to set data held in a GenomicInteractions object. |
| overlapsAny-method | Find overlaps between GRanges and GenomicInteractions objects |
| plotCisTrans | Plots the percentages of cis and trans interactions for a GenomicInteractions object as a donut plot. |
| plotCounts | Plot a bar chart of the number of interactions supported by different numbers of reads in your data. |
| plotDists | Plots a histogram of interaction distances for a GenomicInteractions Object |
| plotInteractionAnnotations | Plot a donut plot of interaction types for an annotated GenomicInteractions object |
| plotSummaryStats | Plot summary statistics for a GenomicInteractions object |
| plotViewpoint | Plot coverage around a virtual 4C viewpoint |
| print-method | Print function for GenomicInteractions |
| removeDups | Remove all but one occurences of a duplicated interaction |
| resetAnnotations | Reset annotations made to a GenomicInteractions object |
| resetAnnotations-method | Reset annotations made to a GenomicInteractions object |
| sameStrand | Tests whether anchors have the same strand. |
| seqinfo-method | Acessing/modifying sequence information for a GenomicInteractions object |
| seqinfo<--method | Acessing/modifying sequence information for a GenomicInteractions object |
| setters | Functions to set data held in a GenomicInteractions object. |
| show-method | Representation function for GenomicInteractions |
| sort-method | Sort GenomicInteractions Object |
| subsetByFeatures | Subset a GenomicInteractions object by features |
| subsetByFeatures-method | Subset a GenomicInteractions object by features |
| sum-method | Return the total number of interactions in a GenomicInteractions GIObject |
| summariseByFeatures | Summary statistics of interactions for a given feature set |
| summariseByFeatures-method | Summary statistics of interactions for a given feature set |
| trim-method | Trim a GenomicInteractions object |
| viewPoint | Virtual 4C viewpoint |
| [ | Standard subsetting methods for GenomicInteractions objects |
| [-method | Standard subsetting methods for GenomicInteractions objects |