calculateTangentNormal: Calculate tangent normal

In lima1/PureCN: Copy number calling and SNV classification using targeted short read sequencing

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

lima1/PureCN documentation built on Sept. 17, 2024, 5:48 a.m.