readSegmentationFile: Read file containing segmentations

In PureCN: Copy number calling and SNV classification using targeted short read sequencing

Description

Read segmentation files produced by DNAcopy, CNVkit or GATK4.

Usage

readSegmentationFile(
  seg.file,
  sampleid,
  model.homozygous = FALSE,
  format,
  zero = FALSE,
  verbose = TRUE
)

Arguments

seg.file	File with segmentation
sampleid	Sampleid, for segmentation files containing multiple samples
model.homozygous	Unless TRUE, checks for very small log2-ratios that cannot happen in samples with normal contamination
format	File format. If missing, derived from the file extension. Currently DNAcopy, and GATK4 (ModelSegments) format supported. CNVkit uses DNAcopy format.
zero	Start position is 0-based. Default is FALSE.
verbose	Verbose output.

Value

A data.frame.

Author(s)

Markus Riester

Examples

seg.file <- system.file("extdata", "example_seg.txt",
    package = "PureCN")
seg <- readSegmentationFile(seg.file, "Sample1")

PureCN documentation built on Nov. 8, 2020, 5:37 p.m.