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]