PureCN (version 1.0.3)

plotBestNormal: Plot the PCA of tumor and its best normal(s)

Description

This function can be used to understand how a best normal is chosen by the findBestNormal function. It can be also used to tune the best normal selection by finding good parameter values for num.normals and pcs.

Usage

plotBestNormal(gatk.normal.files, gatk.tumor.file, 
    normalDB, x = 1, y = 2, col.tumor = "red", col.best.normal = "blue", 
    col.other.normals = "black", ...)

Arguments

gatk.normal.files

GATK coverage file of normal files, typically identified via findBestNormal.

gatk.tumor.file

GATK coverage file of a tumor sample.

normalDB

Database of normal samples, created with createNormalDatabase().

x

PC to be plotted on x-axis.

y

PC to be plotted on y-axis.

col.tumor

Color of tumor in plot.

col.best.normal

Color of best normals in plot.

col.other.normals

Color of best normals in plot.

...

Arguments passed to the plot function.

Value

• Returns NULL

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)
plotBestNormal(gatk.best.normal.file, gatk.tumor.file, normalDB)