createNormalDatabase {PureCN}R Documentation

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. Internally, this function determines the sex of the samples and trains a PCA that is later used for clustering a tumor file with all normal samples in the database.

Usage

createNormalDatabase(normal.coverage.files, sex = NULL,
  max.mean.coverage = NULL, ...)

Arguments

normal.coverage.files

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

sex

character(length(normal.coverage.files)) with sex for all files. F for female, M for male. If all chromosomes are diploid, specify diploid. If NULL, determine from coverage.

max.mean.coverage

Assume that coverages above this value do not necessarily improve copy number normalization. Internally, samples with coverage higher than this value will be normalized to have mean coverage equal to this value. If NULL, use the 80 percentile as cutoff. If NA, does not use a maximum value.

...

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.

Author(s)

Markus Riester

See Also

findBestNormal

Examples


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


[Package PureCN version 1.8.1 Index]