R package for handling genomic interaction data


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Documentation for package ‘GenomicInteractions’ version 1.4.0

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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.

-- A --

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 --

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

-- D --

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

-- E --

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.

-- F --

findOverlaps Find overlaps between GRanges and GenomicInteractions objects
findOverlaps-method Find overlaps between GRanges and GenomicInteractions objects

-- G --

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

-- H --

hg19.refseq.transcripts Human Refseq transcripts from chr 17-18
hic_example_data Example HiC dataset

-- I --

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

-- L --

length-method Get the length of a GenomicInteractions GIObject

-- M --

makeGenomicInteractionsFromFile Function to create GenomicInteraction objects from a file
mm9_refseq_promoters Mouse Refseq promoters from chr 14-15

-- N --

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.

-- O --

overlapsAny-method Find overlaps between GRanges and GenomicInteractions objects

-- P --

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

-- R --

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

-- S --

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

-- T --

trim-method Trim a GenomicInteractions object

-- U --

unique-method unique, GenomicInteractions-method

-- V --

viewPoint Virtual 4C viewpoint

-- misc --

$-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