Man pages for GenomicInteractions
Utilities for handling genomic interaction data

annotateInteractionsAnnotate the interactions in a GInteractions object
annotateRegionsAnnotate regions
asBED-GInteractions-methodCoerce to BED structure
availableDisplayParsThe default display parameters for a track object class can...
calculateDistancesCalculate interaction distances
categoriseInteractionsGet the numbers of interaction types existing in your data
countsBetweenAnchors-methodsSummarise interactions between defined anchors
dot-importHicLibFunction to read in processed Hi-C interaction data generated...
dot-importHomerFunction to read in processed Hi-C interaction data generated...
dot-processChiapetNameFunction to process names relating to interactions stored in...
dot-readBamFunction to read in interaction-data stored in a BAM file
dot-readTwoBamsFunction to read in interaction-data stored in a pair of BAM...
dot-validateInputFunction to validate tabular input
export.bed12Export interactions in BED12 format.
export.bedpeExport interactions in BED Paired-End format.
export.chiasigExport interactions in a BEDPE-like format for use with...
export.igraphExport interactions to an igraph object.
GenomicInteractionsFunction to create a GenomicInteractions object
GenomicInteractions-classA S4 class to represent interactions between genomic regions.
get_binom_ligation_thresholdget self ligation threshold with binomial test
get_self_ligation_thresholdGet self ligation threshold with SD method from Heidari et al
gettersFunctions to access data held in a GenomicInteractions...
GInteractions-subsetByFeatures-methodsSubset a GInteractions object by features
hg19.refseq.transcriptsHuman Refseq transcripts from chr 17-18
hic_example_dataExample HiC dataset
InteractionHelpersInteraction Type Helpers
InteractionTrackConstructor to create an InteractionTrack object
InteractionTrack-classA class to hold chromatin interaction data for a specific...
makeGenomicInteractionsFromFileFunction to create GenomicInteraction objects from a file
mm9_refseq_promotersMouse Refseq promoters from chr 14-15
plotAvgViewpointPlot coverage around a set of virtual 4C viewpoints
plotCisTransPlots the percentages of cis and trans interactions for a...
plotCountsPlot a bar chart of the number of interactions supported by...
plotDistsPlots a histogram of interaction distances for a...
plotInteractionAnnotationsPlot a donut plot of interaction types for an annotated...
plotSummaryStatsPlot summary statistics for a GInteractions object
plotViewpointPlot coverage around a virtual 4C viewpoint
removeDupsRemove all but one occurences of a duplicated interaction
resetAnnotationsReset annotations made to a GInteractions object
sameStrandTests whether anchors have the same strand.
settersFunctions to set data held in a GInteractions object.
sum-GInteractions-methodReturn the total number of interactions in a GInteractions...
summariseByFeaturePairsSummarise the number of interactions between two sets of...
summariseByFeaturesSummary statistics of interactions for a given feature set
thymus_enhPutative enhancers from mouse thymus data
updateObject-GenomicInteractions-methodupdateObject method for GenomicInteractions 1.3.7 and earlier
viewPointVirtual 4C viewpoint
GenomicInteractions documentation built on Nov. 8, 2020, 8:19 p.m.