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| GenomicInteractions-package | GenomicInteractions: A package for analysing chromosome conformation |
| 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 - DEPRECATED |
| annotateAnchors-method | Annotate anchors - DEPRECATED |
| annotateInteractions | Annotate the interactions in a GInteractions object |
| annotateInteractions-method | Annotate the interactions in a GInteractions object |
| annotateRegions | Annotate regions |
| annotateRegions-method | Annotate regions |
| annotationFeatures | Functions to access data held in a GenomicInteractions object. |
| annotationFeatures-method | Functions to access data held in a GenomicInteractions object. |
| asBED-method | Coerce to BED structure |
| availableDisplayPars | The default display parameters for a track object class can be queries using the availableDisplayPars function. |
| calculateDistances | Calculate interaction distances |
| calculateDistances-method | Calculate interaction distances |
| categoriseInteractions | Get the numbers of interaction types existing in your data |
| countsBetweenAnchors | Summarise interactions between defined anchors |
| countsBetweenAnchors-method | Summarise interactions between defined anchors |
| description-method | Functions to access data held in a GenomicInteractions object. |
| description<--method | Functions to set data held in a GInteractions 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. |
| GenomicInteractions | Function to create a GenomicInteractions object |
| GenomicInteractions-class | A S4 class to represent interactions between genomic regions. |
| GenomicInteractions-method | Function to create a GenomicInteractions object |
| 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 GInteractions object. |
| interactionCounts<--method | Functions to set data held in a GInteractions object. |
| InteractionHelpers | Interaction Type Helpers |
| InteractionTrack | Constructor to create an InteractionTrack object |
| InteractionTrack-class | A class to hold chromatin interaction data for a specific genomic region. |
| 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 |
| 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 GInteractions object. |
| name<--method | Functions to set data held in a GInteractions object. |
| plotAvgViewpoint | Plot coverage around a set of virtual 4C viewpoints |
| plotCisTrans | Plots the percentages of cis and trans interactions for a GInteractions 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 GInteractions Object |
| plotInteractionAnnotations | Plot a donut plot of interaction types for an annotated GInteractions object |
| plotSummaryStats | Plot summary statistics for a GInteractions object |
| plotViewpoint | Plot coverage around a virtual 4C viewpoint |
| removeDups | Remove all but one occurences of a duplicated interaction |
| resetAnnotations | Reset annotations made to a GInteractions object |
| resetAnnotations-method | Reset annotations made to a GInteractions object |
| sameStrand | Tests whether anchors have the same strand. |
| setters | Functions to set data held in a GInteractions object. |
| subsetByFeatures | Subset a GInteractions object by features |
| subsetByFeatures-method | Subset a GInteractions object by features |
| sum-method | Return the total number of interactions in a GInteractions GIObject |
| summariseByFeaturePairs | Summarise the number of interactions between two sets of features. |
| summariseByFeaturePairs-method | Summarise the number of interactions between two sets of features. |
| summariseByFeatures | Summary statistics of interactions for a given feature set |
| summariseByFeatures-method | Summary statistics of interactions for a given feature set |
| thymus_enh | Putative enhancers from mouse thymus data |
| updateObject-method | updateObject method for GenomicInteractions 1.3.7 and earlier |
| viewPoint | Virtual 4C viewpoint |