Man pages for ComputationalRegulatoryGenomicsICL/GenomicInteractions
Utilities for handling genomic interaction data
| annotateInteractions | Annotate the interactions in a GInteractions object |
| annotateRegions | Annotate regions |
| asBED-GInteractions-method | Coerce to BED structure |
| availableDisplayPars | The default display parameters for a track object class can... |
| calculateDistances | Calculate interaction distances |
| categoriseInteractions | Get the numbers of interaction types existing in your data |
| countsBetweenAnchors-methods | Summarise interactions between defined anchors |
| dot-importHicLib | Function to read in processed Hi-C interaction data generated... |
| dot-importHomer | Function to read in processed Hi-C interaction data generated... |
| dot-processChiapetName | Function to process names relating to interactions stored in... |
| dot-readBam | Function to read in interaction-data stored in a BAM file |
| dot-readTwoBams | Function to read in interaction-data stored in a pair of BAM... |
| dot-validateInput | Function to validate tabular input |
| export.bed12 | Export interactions in BED12 format. |
| export.bedpe | Export interactions in BED Paired-End format. |
| export.chiasig | Export interactions in a BEDPE-like format for use with... |
| export.igraph | 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-package | GenomicInteractions |
| 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 |
| getters | Functions to access data held in a GenomicInteractions... |
| GInteractions-subsetByFeatures-methods | Subset a GInteractions object by features |
| hg19.refseq.transcripts | Human Refseq transcripts from chr 17-18 |
| hic_example_data | Example HiC dataset |
| InteractionHelpers | Interaction Type Helpers |
| InteractionTrack | Constructor to create an InteractionTrack object |
| InteractionTrack-class | A class to hold chromatin interaction data for a specific... |
| makeGenomicInteractionsFromFile | Function to create GenomicInteraction objects from a file |
| mm9_refseq_promoters | Mouse Refseq promoters from chr 14-15 |
| plotAvgViewpoint | Plot coverage around a set of virtual 4C viewpoints |
| plotCisTrans | Plots the percentages of cis and trans interactions for a... |
| plotCounts | Plot a bar chart of the number of interactions supported by... |
| plotDists | Plots a histogram of interaction distances for a... |
| plotInteractionAnnotations | Plot a donut plot of interaction types for an annotated... |
| 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 |
| sameStrand | Tests whether anchors have the same strand. |
| setters | Functions to set data held in a GInteractions object. |
| sum-GInteractions-method | Return the total number of interactions in a GInteractions... |
| summariseByFeaturePairs | Summarise the number of interactions between two sets of... |
| summariseByFeatures | Summary statistics of interactions for a given feature set |
| thymus_enh | Putative enhancers from mouse thymus data |
| updateObject-GenomicInteractions-method | updateObject method for GenomicInteractions 1.3.7 and earlier |
| viewPoint | Virtual 4C viewpoint |
