calculateLogRatio {PureCN} | R Documentation

## Calculate coverage log-ratio of tumor vs. normal

### Description

This function is automatically called by `runAbsoluteCN` when normal and tumor coverage are provided (and not a segmentation file or target-level log-ratios). This function is therefore normally not called by the user.

### Usage

    calculateLogRatio(normal, tumor)

### Arguments

`normal` | Normal coverage read in by the `readCoverageFile` function.
`tumor` | Tumor coverage read in by the `readCoverageFile` function.

### Value

`numeric(length(tumor))`, tumor vs. normal copy number log-ratios for all targets.

### Author(s)

Markus Riester

### Examples

    normal.coverage.file <- system.file("extdata", "example_normal.txt",
        package="PureCN")
    tumor.coverage.file <- system.file("extdata", "example_tumor.txt",
        package="PureCN")
    normal <- readCoverageFile(normal.coverage.file)
    tumor <- readCoverageFile(tumor.coverage.file)
    log.ratio <- calculateLogRatio(normal, tumor)

[Package PureCN version 1.12.2 Index]