focalAmpliconDupRanges: Identify lower copy focal amplicons (possibly duplicatons)...

In cancer-genomics/trellis: Somatic structural variant analysis

Identify lower copy focal amplicons (possibly duplicatons) not already annotated as amplicons and not contained within the germline filters

Description

Select all duplicated segments (see isDuplication) less than 'maxgap' kb from the seed amplicons of the graph that are not within a germline CNV or outlier. Germline CNVs and outliers can be conveniently extracted from the graph object as given in the examples.

Usage

focalAmpliconDupRanges(object, params)

Arguments

object	A AmpliconGraph
params	a list of parameters such as that generated by ampliconParams.

Value

a reduced GRanges of lower-copy amplicons

See Also

ampliconParams

Examples

  ## load a previously saved AmpliconGraph from a regression unit test
  ## Not run: 
    path <- system.file("testthat", package="trellis")
    ag <- readRDS(file.path(path, "addFocalDups.ffab104.rds"))
    params <- ampliconParams()
    focalAmpliconDupRanges(ag, params)

## End(Not run)

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