filterRearExperiment: Exclude linked tag cluster that overlap with germline CNVs or...

In cancer-genomics/trellis: Somatic structural variant analysis

Exclude linked tag cluster that overlap with germline CNVs or other sequence artifacts

Description

This is a wrapper for filterRearrangementList (somatic) and filterGermlineRear (germline). The filtered rearrangements are saved to an intermediate file. If the file already exists, the saved result is read from disk. To rerun the filtering step, the intermediate files must be removed. See examples.

Usage

filterRearExperiment(
  x,
  dirs,
  cnvs,
  germline_filters,
  rear_filter,
  rp = RearrangementParams()
)

Arguments

x	a RearrangementList
dirs	a DataPaths object
cnvs	a list of deletions and amplicons
germline_filters	a GRanges object of germline filters
rear_filter	a GRanges object of rearrangements found in germline
rp	a RearrangementParams object

Details

REFACTORING: Too many arguments. Unclear distinction between germline_filters and rear_filter. Should have a separate function for germline, or have an S4 germline class.

The amplicons (amps) and deletions (del.gr) will be subset by the mcols variable 'id'.

Value

a RearrangementList

See Also

See filterRearrangementList for filtering somatic rearrangements and filterGermlineRear for filtering germline rearrangements. See listCNVs for listing the deletions and amplicons for a given sample.

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