readLogRatioFile {PureCN} | R Documentation

## Read file containing interval-level log2 tumor/normal ratios

### Description

Read log2 ratio file produced by external tools like The Genome Analysis Toolkit version 4.

### Usage

    readLogRatioFile(file, format, zero = NULL)

### Arguments

`file` | Log2 coverage file.
`format` | File format. If missing, derived from the file extension. Currently GATK4 DenoiseReadCounts format supported. A simple GATK3-style format, two columns with coordinates as string in format chr:start-stop in first and log2-ratio in second is also supported.
`zero` | Start position is 0-based. Default is `FALSE` for GATK, `TRUE` for BED file based intervals.

### Value

A `GRange` with the log2 ratio.

### Author(s)

Markus Riester

### Examples

    logratio.file <- system.file("extdata", "example_gatk4_denoised_cr.tsv.gz",
        package = "PureCN")
    logratio <- readLogRatioFile(logratio.file)

[Package PureCN version 1.20.0 Index]