calculateLogRatio: Calculate coverage log-ratio of tumor vs. normal

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

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

lima1/PureCN documentation built on Sept. 17, 2024, 5:48 a.m.