numberLinkingRP-methods: Calculate the number of read pairs that link two clusters of...

In cancer-genomics/trellis: Somatic structural variant analysis

Calculate the number of read pairs that link two clusters of improper reads

Description

Clusters of improper read pairs can be linked by the mates of the improper reads that belong to these clusters. This function computes the number of improperly paired reads that link two clusters. The number of read pairs that would link two clusters in a bona fide somatic rearrangement depends on the depth of sequencing. For 30x coverage, we require at least 5 linking read pairs.

Usage

numberLinkingRP(object)

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

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

Value

a numeric vector

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