AmpliconGraph-class: A class for representing somatic amplicons

In cancer-genomics/trellis: Somatic structural variant analysis

A class for representing somatic amplicons

Description

Somatic amplicons are often grouped by a bridge-breakage-fusion cycles. We represent the set of amplicons identified for a sample as a graph with amplicons as the nodes. An edge drawn between two nodes indicates that five or more read pairs with aberrant spacing support the link between these amplicons. As the class is an extension of the graphNEL class, plot methods to visualize the graph are readily available.

Usage

amplicons(object)

amplicons(object) <- value

ampliconRanges(object)

ampliconRanges(object) <- value

assemblyGaps(object)

driver(object)

graph(object)

graph(object) <- value

isAmplicon(object)

isSomatic(object)

nonampliconRanges(object)

queryRanges(object)

queryRanges(object) <- value

ampliconNames(amplicons)

## S4 method for signature 'character,AmpliconGraph,ANY'
addNode(node, object, edges)

## S4 method for signature 'AmpliconGraph'
amplicons(object)

## S4 replacement method for signature 'AmpliconGraph'
amplicons(object) <- value

## S4 method for signature 'AmpliconGraph'
assemblyGaps(object)

## S4 replacement method for signature 'AmpliconGraph'
ampliconRanges(object) <- value

## S4 method for signature 'AmpliconGraph'
ampliconRanges(object)

## S4 method for signature 'GRanges'
ampliconRanges(object)

## S4 method for signature 'AmpliconGraph'
graph(object)

## S4 method for signature 'AmpliconGraph'
driver(object)

## S4 method for signature 'AmpliconGraph'
edges(object, which, ...)

## S4 replacement method for signature 'AmpliconGraph'
graph(object) <- value

## S4 method for signature 'AmpliconGraph'
isAmplicon(object)

## S4 method for signature 'GRanges'
isAmplicon(object)

## S4 method for signature 'GRanges'
isSomatic(object)

## S4 method for signature 'AmpliconGraph'
length(x)

## S4 method for signature 'AmpliconGraph'
nodes(object)

## S4 replacement method for signature 'AmpliconGraph,ANY'
names(x) <- value

## S4 method for signature 'AmpliconGraph'
nonampliconRanges(object)

## S4 method for signature 'GRanges'
nonampliconRanges(object)

## S4 method for signature 'AmpliconGraph'
numEdges(object)

## S4 method for signature 'AmpliconGraph'
numNodes(object)

## S4 method for signature 'AmpliconGraph'
queryRanges(object)

## S4 replacement method for signature 'AmpliconGraph'
queryRanges(object) <- value

## S4 method for signature 'AmpliconGraph'
ranges(x, use.names = TRUE, use.mcols = FALSE, ...)

## S4 replacement method for signature 'AmpliconGraph'
ranges(x) <- value

Arguments

object	a AmpliconGraph object
value	genomic amplicon intervals as a GRanges object
amplicons	genomic intervals of amplicons as a GRanges object
node	name of amplicon
edges	name of edge (e.g., concatenate two amplicon names)
which	ignored
...	ignored
x	a AmpliconGraph
use.names	logical
use.mcols	logical

See Also

See sv_amplicon_exp for generating a list of AmpliconGraphs for an experiment.

cancer-genomics/trellis documentation built on June 8, 2024, 6:01 a.m.