calculateTangentNormal {PureCN} | R Documentation

## Calculate tangent normal

### Description

Reimplementation of GATK4 denoising. Please cite the relevant GATK publication if you use this in a publication.

### Usage

    calculateTangentNormal(
      tumor.coverage.file,
      normalDB,
      num.eigen = 20,
      ignore.sex = FALSE,
      sex = NULL
    )

### Arguments

`tumor.coverage.file` | Coverage file or data of a tumor sample.
`normalDB` | Database of normal samples, created with `createNormalDatabase`.
`num.eigen` | Number of eigen vectors used.
`ignore.sex` | If `FALSE`, detects sex of sample and returns best normals with matching sex.
`sex` | Sex of sample. If `NULL`, determine with `getSexFromCoverage` and default parameters. Valid values are `F` for female, `M` for male. If all chromosomes are diploid, specify `diploid`.

### Author(s)

Markus Riester

### See Also

`createNormalDatabase`

### Examples

    tumor.coverage.file <- system.file('extdata', 'example_tumor.txt',
        package='PureCN')
    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)
    pool <- calculateTangentNormal(tumor.coverage.file, normalDB)

[Package PureCN version 1.20.0 Index]