makeAGraph: Initialize a graph object for amplicon analyses

In cancer-genomics/trellis: Somatic structural variant analysis

Initialize a graph object for amplicon analyses

Description

Initialize a graph object for amplicon analyses

Usage

makeAGraph(segs, af, params)

Arguments

segs	a GRanges object from the segmentation of the normalized coverage
af	a list of germline filters
params	a list of parameters

See Also

ampliconParams

Examples

  library(svfilters.hg19)
  library(svbams)
  library(Rsamtools)
  data(germline_filters)
  ##
  ## read in some CNVs
  ##
  cv.extdata <- system.file("extdata", package="svbams")
  segs <- readRDS(file.path(cv.extdata, "cgov44t_segments.rds"))
  extdata <- system.file("extdata", package="svbams")
  bview <- BamViews(bamPaths=file.path(extdata, "cgov44t_revised.bam"))
  params <- ampliconParams()
  germline_filters[["germline_cnv"]] <- GRanges()
  germline_filters[["outliers"]] <- GRanges()
  makeAGraph(segs, germline_filters, params)

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