testAllelicBalanceByBAFs: Tests for allelic balance in a genomic region

In HenrikBengtsson/aroma.cn: Copy-Number Analysis of Large Microarray Data Sets

Tests for allelic balance in a genomic region

Description

Tests for allelic balance in a genomic region.

Usage

## Default S3 method:
testAllelicBalanceByBAFs(betaT, muN, flavor=c("var", "mean"), ..., verbose=FALSE)

Arguments

betaT	A numeric vector of J tumor allele B fractions (BAFs).
muN	A numeric vector of J normal (germline) genotypes.
flavor	A character specifying the type of test to be performed.
...	Not used.
verbose	See Verbose.

Value

A list of class "htest".

Author(s)

Henrik Bengtsson, Pierre Neuvial

Examples

if (Sys.getenv("_R_CHECK_FULL_") != "" && require("PSCBS")) {

# Load example ASCN data
data <- PSCBS::exampleData("paired.chr01");

# PSCBS segmentation
fit <- segmentByPairedPSCBS(data, verbose=-10);

# Normalize
fitN <- normalizeBAFsByRegions(fit, verbose=-10);

fitN2 <- callAllelicBalanceByBAFs(fitN, verbose=-10);
print(fitN2);

} # if (require("PSCBS"))

HenrikBengtsson/aroma.cn documentation built on Feb. 20, 2024, 9:15 p.m.