createNormalDatabase {PureCN} | R Documentation |
Function to create a database of normal samples, used to normalize tumor coverages.
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, ...)
normal.coverage.files |
Vector with file names pointing to coverage files of normal samples. |
sex |
|
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 |
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 |
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)