findBestNormal {PureCN}R Documentation

Find best normal sample in database

Description

Function to find the best matching normal for a provided tumor sample. This function is deprecated and most features are not relevant with the replacement function calculateTangentNormal.

Usage

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, ...)

Arguments

tumor.coverage.file

Coverage file or data of a tumor sample.

normalDB

Database of normal samples, created with createNormalDatabase.

pcs

Principal components to use for distance calculation.

num.normals

Return the num.normals best normals.

ignore.sex

If FALSE, detects sex of sample and returns best normals with matching sex.

sex

Sex of sample. If NULL, determine with getSexFromCoverage and default parameters. Valid values are F for female, M for male. If all chromosomes are diploid, specify diploid.

normal.coverage.files

Only consider these normal samples. If NULL, use all in the database. Must match normalDB$normal.coverage.files.

pool

If TRUE, use poolCoverage to pool best normals.

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 poolCoverage.

Value

Filename of the best matching normal.

Author(s)

Markus Riester

See Also

createNormalDatabase getSexFromCoverage


[Package PureCN version 1.10.0 Index]