createNormalDatabase: Create database of normal samples

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

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.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)

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