improper-methods: Accessor for improper read pairs

In cancer-genomics/trellis: Somatic structural variant analysis

Accessor for improper read pairs

Description

Extract the improperly paired reads. Reads are flagged as improper by the alignment algorithm. Typically, this indicates that the separation between a read and its mate is larger than expected, the orientation of the read and its mate is different from that anticipated in the reference genome, or the reads align to different chromosomes.

Usage

improper(object)

improper(object) <- value

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

## S4 replacement method for signature 'StructuralVariant,GAlignmentPairs'
improper(object) <- value

## S4 replacement method for signature 'Rearrangement,GAlignmentPairs'
improper(object) <- value

Arguments

object	a Rearrangement or StructuralVariant object
value	a GAlignmentPairs object

See Also

Rearrangement

cancer-genomics/trellis documentation built on Feb. 2, 2023, 7:04 p.m.