sv_amplicon_exp: Identify somatic amplicons and grouped amplicons

In cancer-genomics/trellis: Somatic structural variant analysis

Identify somatic amplicons and grouped amplicons

Description

This function identifies focal, somatic amplifications. As amplicons are often grouped by the bridge-fusion-breakage cycles, we represent the set of somatic amplicons identified for a sample as a graph. The nodes of the graph are the amplicons and the edges are the links between amplicons informed by paired reads. This function is a wrapper for sv_amplicons that constructs an AmpliconGraph for a given sample. As with the other *Experiment functions, sv_amplicon_exp saves the AmpliconGraph computed for each sample as in intermediate file for quick recall. If the file exists, this function reads the serialized R object from disk. To generate an AmpliconGraph de novo, one must first delete the intermediate files (see examples).

Usage

sv_amplicon_exp(
  dirs,
  bviews,
  grl,
  amplicon_filters,
  params = ampliconParams(),
  transcripts
)

Arguments

dirs	character-vector of file paths for storing intermediate files
bviews	A BamViews object
grl	A GRangesList of the segmented genomes (each element is the GRanges for a sample)
amplicon_filters	A list of germline filters and parameters. See the germline_filters object in the package svfilters.<build>.
params	a list of parameters for the amplicon analysis
transcripts	a GRanges object of the transcripts.

See Also

See AmpliconGraph for methods associated with the class and sv_amplicons for construction of an AmpliconGraph for a single sample.

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