createNormalDatabase {PureCN} | R Documentation

## Create database of normal samples

### Description

Function to create a database of normal samples, used to normalize tumor coverages.

### Usage

    createNormalDatabase(
      normal.coverage.files,
      sex = NULL,
      coverage.outliers = c(0.25, 4),
      min.coverage = 0.25,
      max.missing = 0.03,
      low.coverage = 15,
      optimal.off.target.counts = 120,
      plot = FALSE,
      ...
    )

### 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.
`coverage.outliers` | Exclude samples with coverages below or above the specified cutoffs (fractions of the normal sample coverages median). Only for databases with more than 5 samples.
`min.coverage` | Exclude intervals with coverage lower than the specified fraction of the chromosome median in the pool of normals.
`max.missing` | Exclude intervals with zero coverage in the specified fraction of normal samples.
`low.coverage` | Specifies the maximum number of total reads (NOT average coverage) to call a target low coverage.
`optimal.off.target.counts` | Used to suggest an optimal off-target interval width (BETA).
`plot` | Diagnostics plot, useful to tune parameters.
`...` | Arguments passed to the `prcomp` function.

### Value

A normal database that can be used in the `calculateTangentNormal` function to retrieve a coverage normalization sample for a given tumor sample.

### Author(s)

Markus Riester

### See Also

`calculateTangentNormal`

### 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 1.22.2 Index]