calculateTangentNormal {PureCN} | R Documentation |
Reimplementation of GATK4 denoising. Please cite the relevant GATK publication if you use this in a publication.
calculateTangentNormal( tumor.coverage.file, normalDB, num.eigen = 20, ignore.sex = FALSE, sex = NULL )
tumor.coverage.file |
Coverage file or data of a tumor sample. |
normalDB |
Database of normal samples, created with
|
num.eigen |
Number of eigen vectors used. |
ignore.sex |
If |
sex |
Sex of sample. If |
Markus Riester
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)