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

In lima1/PureCN: Copy number calling and SNV classification using targeted short read sequencing

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)

lima1/PureCN documentation built on April 3, 2024, 7:56 a.m.