readSegmentationFile {PureCN} | R Documentation

## Read file containing segmentations

### 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")

[Package PureCN version 1.22.2 Index]