filterRearrangementList: Applies several filters for somatic rearrangements

In cancer-genomics/trellis: Somatic structural variant analysis

Applies several filters for somatic rearrangements

Description

Removes rearrangement intervals that overlap with previously identified somatic amplicons and deletions, as well as germline CNVs and rearrangements.

Usage

filterRearrangementList(
  object,
  params,
  amps,
  del.gr,
  rear_filter,
  germline_filters = GRanges(),
  return_stats = FALSE
)

Arguments

object	A RearrangementList
params	A RearrangementParams object
amps	GRanges of amplicons
del.gr	GRanges of deletions
rear_filter	GRanges object of germline rearrangements
germline_filters	GRanges of germline CNVs and sequence filters
return_stats	a length-one logical vector. For internal use.

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