readLogRatioFile: Read file containing interval-level log2 tumor/normal ratios

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

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)

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