PureCN (version 1.0.3)

createNormalDatabase: Create database of normal samples

Description

Function to create a database of normal samples, used to find a good match for tumor copy number normalization.

Usage

createNormalDatabase(gatk.normal.files, ...)

Arguments

gatk.normal.files

Vector with file names pointing to GATK coverage files of normal samples.

...

Arguments passed to the prcomp function.

Value

• A normal database that can be used in the findBestNormal function to retrieve good matching normal samples for a given tumor sample.

Examples

gatk.normal.file <- system.file("extdata", "example_normal.txt", 
    package="PureCN")
gatk.normal2.file <- system.file("extdata", "example_normal2.txt", 
    package="PureCN")
gatk.normal.files <- c(gatk.normal.file, gatk.normal2.file)
normalDB <- createNormalDatabase(gatk.normal.files)

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