compileCopyCountSegments: Compile segments across samples

In exomeCopy: Copy number variant detection from exome sequencing read depth

Description

A short function which extracts the segments of constant copy count using the copyCountSegments function on a named list of named lists containing fitted ExomeCopy objects. See vignette for a full example of multiple samples and chromosomes.

Usage

  compileCopyCountSegments(fit.list)

Arguments

fit.list

A named list of named lists. The outer list indexes patients, while the inner list indexes sequences/chromosomes.

Value

A GRanges object of all segments across samples and chromosomes.

Examples

  example(exomeCopy)

  # this function requires a named list of named lists
  # as constructed in the vignette
  fit.list <- list(sample1 = list(chr1 = fit))
  CNV.segments <- compileCopyCountSegments(fit.list)

exomeCopy documentation built on Nov. 8, 2020, 7:45 p.m.