Rearrangement-class: A class for storing rearrangement data

In cancer-genomics/trellis: Somatic structural variant analysis

A class for storing rearrangement data

Description

This class contains the genomic intervals corresponding to improper read clusters. Improper read clusters that are linked are candidate rearrangements. The linking is represented by a GRanges object with a 'linked.to' variable in the mcols. All improper reads belonging to a cluster, irrespective of whether they link two clusters, are included and indexed to facilitate subsetting operations.

Usage

partitioning(object)

## S4 method for signature 'Rearrangement'
partitioning(object)

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

## S4 method for signature 'Rearrangement'
names(x)

## S4 method for signature 'Rearrangement,ANY,ANY,ANY'
x[i, j, ..., drop = FALSE]

## S4 method for signature 'Rearrangement'
type(x)

## S4 method for signature 'RearrangementList'
type(x)

Arguments

x	a Rearrangement object
i	a logical vector
j	ignored
...	ignored
drop	ignored

Value

a Rearrangement object

Slots

linkedBins

a GRanges object with 'linked.to' in the element metadata (mcols)

modal_rearrangement

character string indicating type of rearrangement

improper

a GAlignmentPairs object of the improper read pairs

partitioning

integer vector

link1id

character string label for first read cluster

link2id

character string label for second read cluster

tags

a GRanges object of single tags

tag_map_to_linked_bin

an integer vector keeping track of which tags belong to a linked bin

modal_rearrangement

charactering string of the modal rearrangemnt type

percent_rearrangement

length-one numeric vector indicating the percentage of improper read pairs for a linked bin that belong to the modal rearrangement

fraction_linking_tags

the fraction of all tags for a linked bin that link the two tag clusters

split_reads

a GRanges object of the split read alignments

cancer-genomics/trellis documentation built on Aug. 20, 2024, 5:48 p.m.