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| GenomicInteractions-package | A package for looking at genomic interaction data. |
| 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. |
| 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 |
| count | Functions to access data held in a GenomicInteractions object. |
| count-method | Functions to access data held in a GenomicInteractions object. |
| 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.igraph | Export interactions to an igraph object. |
| export.igraph-method | Export interactions to an igraph object. |
| FDR | Functions to access data held in a GenomicInteractions object. |
| FDR-method | Functions to access data held in a GenomicInteractions object. |
| FDR<- | Functions to set data held in a GenomicInteractions object. |
| FDR<--method | Functions to set data held in a GenomicInteractions object. |
| findOverlaps | Find overlaps between a GRanges and a GenomicInteractions object |
| findOverlaps-method | Find overlaps between a GRanges and a GenomicInteractions object |
| genomeName | Functions to access data held in a GenomicInteractions object. |
| genomeName-method | Functions to access data held in a GenomicInteractions object. |
| GenomicInteractions | Function to create GenomicInteraction objects. |
| GenomicInteractions-class | A S4 class to represent interactions between genomic regions. |
| getters | Functions to access data held in a GenomicInteractions object. |
| hg19.refseq.transcripts | Human Refseq transcripts from chr 17-18 |
| hic_example_data | Example HiC dataset |
| 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 |
| 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. |
| normalisedCount | Functions to access data held in a GenomicInteractions object. |
| normalisedCount-method | Functions to access data held in a GenomicInteractions object. |
| normalisedCount<- | Functions to set data held in a GenomicInteractions object. |
| normalisedCount<--method | Functions to set data held in a GenomicInteractions object. |
| 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 |
| plotRegion | Plot interactions within a specified region. |
| plotRegion-method | Plot interactions within a specified region. |
| plotSummaryStats | Plot summary statistics for a GenomicInteractions object |
| print-method | Print function for GenomicInteractions |
| pValue | Functions to access data held in a GenomicInteractions object. |
| pValue-method | Functions to access data held in a GenomicInteractions object. |
| pValue<- | Functions to set data held in a GenomicInteractions object. |
| pValue<--method | Functions to set data held in a GenomicInteractions object. |
| resetAnnotations | Reset annotations made to a GenomicInteractions object |
| resetAnnotations-method | Reset annotations made to a GenomicInteractions object |
| setters | Functions to set data held in a GenomicInteractions object. |
| show-method | Representation function for GenomicInteractions |
| 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 |
| viewPoint | Plot coverage of interactions originating at a given viewpoint. |
| viewPointAverage | Plot coverage of interactions originating at a given set of viewpoints. |
| [ | Standard subsetting methods for GenomicInteractions objects |
| [-method | Standard subsetting methods for GenomicInteractions objects |