findBestNormal {PureCN} | R Documentation |
Function to find the best matching normal for a provided tumor sample.
findBestNormal(tumor.coverage.file, normalDB, pcs = 1:3, num.normals = 1, ignore.sex = FALSE, sex = NULL, normal.coverage.files = NULL, pool = FALSE, pool.weights = c("voom", "equal"), plot.pool = FALSE, ...)
tumor.coverage.file |
Coverage file or data of a tumor sample. |
normalDB |
Database of normal samples, created with
|
pcs |
Principal components to use for distance calculation. |
num.normals |
Return the |
ignore.sex |
If |
sex |
Sex of sample. If |
normal.coverage.files |
Only consider these normal samples. If
|
pool |
If |
pool.weights |
Either find good pooling weights by optimization or weight all best normals equally. |
plot.pool |
Allows the pooling function to create plots. |
... |
Additional arguments passed to |
Filename of the best matching normal.
Markus Riester
createNormalDatabase getSexFromCoverage
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) tumor.coverage.file <- system.file("extdata", "example_tumor.txt", package="PureCN") best.normal.coverage.file <- findBestNormal(tumor.coverage.file, normalDB) pool <- findBestNormal(tumor.coverage.file, normalDB, num.normals=2, pool=TRUE)