createNormalDatabase {PureCN} | R Documentation |
Function to create a database of normal samples, used to normalize tumor coverages.
createNormalDatabase( normal.coverage.files, sex = NULL, coverage.outliers = c(0.25, 4), min.coverage = 0.25, max.missing = 0.03, low.coverage = 15, plot = FALSE, ... )
normal.coverage.files |
Vector with file names pointing to coverage files of normal samples. |
sex |
|
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. |
plot |
Diagnostics plot, useful to tune parameters. |
... |
Arguments passed to the |
A normal database that can be used in the
calculateTangentNormal
function to retrieve a coverage
normalization sample for a given tumor sample.
Markus Riester
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)