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

View source: R/calculateLogRatio.R

calculateLogRatioR 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.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.