PureCN (version 1.0.3)

findBestNormal: Find best normal sample in database

Description

Function to find the best matching normal for a provided tumor sample.

Usage

findBestNormal(gatk.tumor.file, normalDB, pcs = 1:3, 
    num.normals = 1, ignore.sex = FALSE, verbose = TRUE)

Arguments

gatk.tumor.file

GATK coverage file of a tumor sample.

normalDB

Database of normal samples, created with createNormalDatabase().

pcs

Principal components to use for distance calculation.

num.normals

Return the num.normals best normals.

ignore.sex

If FALSE, detects sex of sample and returns best normals with matching sex.

verbose

Verbose output.

Value

• Filename of the best matching normal.

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)

gatk.tumor.file <- system.file("extdata", "example_tumor.txt", 
    package="PureCN")
gatk.best.normal.file <- findBestNormal(gatk.tumor.file, normalDB)