Rearrangement-class: Accessor for the combination of strands involved in a...

In cancer-genomics/trellis: Somatic structural variant analysis

Accessor for the combination of strands involved in a rearrangement

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)

type(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(object)

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

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 Feb. 2, 2023, 7:04 p.m.