A C D E F G H I L M N O P R S T U V misc
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. |
availableDisplayPars | The default display parameters for a track object class can be queries using the availableDisplayPars function. |
c | Combine GenomicInteractions Methods |
c-method | Combine GenomicInteractions Methods |
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 |
countOverlaps-method | Find overlaps between GRanges and GenomicInteractions objects |
countsBetweenAnchors | Summarise Interactions between defined anchors |
countsBetweenAnchors-method | Summarise Interactions between defined anchors |
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. |
duplicated-method | duplicated, GenomicInteractions-method |
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. |
findOverlaps | Find overlaps between GRanges and GenomicInteractions objects |
findOverlaps-method | Find overlaps between GRanges and GenomicInteractions objects |
GenomicInteractions | Function to create a GenomicInteraction object |
GenomicInteractions-class | A S4 class to represent interactions between genomic regions. |
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 GenomicInteractions object. |
interactionCounts<--method | Functions to set data held in a GenomicInteractions 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 |
length-method | Get the length of a GenomicInteractions GIObject |
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 GenomicInteractions object. |
name<--method | Functions to set data held in a GenomicInteractions object. |
overlapsAny-method | Find overlaps between GRanges and GenomicInteractions objects |
plotAvgViewpoint | Plot coverage around a set of virtual 4C viewpoints |
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 |
plotSummaryStats | Plot summary statistics for a GenomicInteractions object |
plotViewpoint | Plot coverage around a virtual 4C viewpoint |
print-method | Print function for GenomicInteractions |
removeDups | Remove all but one occurences of a duplicated interaction |
resetAnnotations | Reset annotations made to a GenomicInteractions object |
resetAnnotations-method | Reset annotations made to a GenomicInteractions object |
sameStrand | Tests whether anchors have the same strand. |
seqinfo-method | Acessing/modifying sequence information for a GenomicInteractions object |
seqinfo<--method | Acessing/modifying sequence information for a GenomicInteractions object |
setters | Functions to set data held in a GenomicInteractions object. |
show-method | Representation function for GenomicInteractions |
sort-method | Sort GenomicInteractions Object |
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 |
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 |
trim-method | Trim a GenomicInteractions object |
unique-method | unique, GenomicInteractions-method |
viewPoint | Virtual 4C viewpoint |
$-method | Quick access to GenomicInteractions metadata columns |
$<--method | Quick access to GenomicInteractions metadata columns |
[ | Standard subsetting methods for GenomicInteractions objects |
[-method | Standard subsetting methods for GenomicInteractions objects |