calculateTangentNormal: Calculate tangent normal

View source: R/createNormalDatabase.R

calculateTangentNormalR 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.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.