createNormalDatabase {PureCN}R Documentation

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,
  max.mean.coverage = NULL, coverage.outliers = c(0.25, 4),
  min.coverage = 0.25, max.missing = 0.03, low.coverage = 15, ...)

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.

max.mean.coverage

Assume that coverages above this value do not necessarily improve copy number normalization. Internally, samples with coverage higher than this value will be normalized to have mean coverage equal to this value. If NULL, use the 80 percentile as cutoff. If NA, does not use a maximum value.

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 targets with coverage lower than the specified fraction of the chromosome median in the pool of normals.

max.missing

Exclude targets 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.

...

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", 
    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)


[Package PureCN version 1.10.0 Index]