GenomicInteractions-package | GenomicInteractions |
.importHicLib | Function to read in processed Hi-C interaction data generated by hiclib |
.importHomer | Function to read in processed Hi-C interaction data generated by HOMER |
.processChiapetName | Function to process names relating to interactions stored in bed12 formats. |
.readBam | Function to read in interaction-data stored in a BAM file |
.readTwoBams | Function to read in interaction-data stored in a pair of BAM files |
.validateInput | Function to validate tabular input |
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. |
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 |