linkedBins-methods: Accessor for clusters of reads belonging to improper read...

In cancer-genomics/trellis: Somatic structural variant analysis

Accessor for clusters of reads belonging to improper read pairs that are linked.

Description

Clusters of improper reads that are linked by the read pairs are suggestive of a new (somatic) sequence junction not present in the reference genome. The linking is represented by a GRanges object with an interval demarcating the boundaries of a cluster of improper tags. The tag cluster that is linked by the pairing information is put in the element metadata (mcols) of the GRanges object.

Usage

linkedBins(object)

linkedBins(object) <- value

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

## S4 replacement method for signature 'Rearrangement'
linkedBins(object) <- value

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

## S4 replacement method for signature 'RearrangementList'
linkedBins(object) <- value

Arguments

object	a Rearrangement object
value	a GRanges object with a column linked.to in the element metadata.

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