getSequenceOfReads-methods: Extract sequences of reads supporting rearrangements from a...

getSequenceOfReadsR Documentation

Extract sequences of reads supporting rearrangements from a bam file

Description

Extract sequences of reads supporting rearrangements from a bam file

Usage

getSequenceOfReads(
  object,
  bam.file,
  params = RearrangementParams(),
  MAX = 25L,
  build
)

## S4 method for signature 'Rearrangement'
getSequenceOfReads(
  object,
  bam.file,
  params = RearrangementParams(),
  MAX = 25L,
  build
)

## S4 method for signature 'StructuralVariant'
getSequenceOfReads(
  object,
  bam.file,
  params = RearrangementParams(),
  MAX = 25L,
  build
)

## S4 method for signature 'RearrangementList'
getSequenceOfReads(
  object,
  bam.file,
  params = RearrangementParams(),
  MAX = 25L,
  build
)

Arguments

object

a Rearrangement or RearrangementList object

bam.file

complete path to BAM file

params

a RearrangementParams object

MAX

the maximum number of read pairs to extract for a rearrangement. If the number of read pairs supporting a rearrangement is greater than MAX, a random sample of MAX supporting read pairs is returned.

build

the reference genome buld that reads were aligned to. Currently supported builds include "hg19" and "hg18".

Value

a data.frame


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