createNormalDatabase {PureCN} | R Documentation |
Function to create a database of normal samples, used to find a good match for tumor copy number normalization. Internally, this function determines the sex of the samples and trains a PCA that is later used for clustering a tumor file with all normal samples in the database.
createNormalDatabase(normal.coverage.files, sex = NULL, max.mean.coverage = NULL, ...)
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 |
... |
Arguments passed to the |
A normal database that can be used in the
findBestNormal
function to retrieve good matching normal
samples 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)