getSequenceOfReads-methods: Extract sequences of reads supporting rearrangements from a...
In cancer-genomics/trellis: Somatic structural variant analysis

getSequenceOfReads

R 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".