callCopyNeutralRegions.PairedPSCBS: Calls regions that are copy neutral

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

Calls regions that are copy neutral

Description

Calls regions that are copy neutral from the allele B fractions (BAF).

Usage

## S3 method for class 'PairedPSCBS'
callCopyNeutralRegions(fit, ...)

Arguments

fit	A PairedPSCBS fit object as returned by segmentByPairedPSCBS.
...	Additional arguments passed to callCopyNeutral.PairedPSCBS.

Value

Returns a PairedPSCBS fit object where a column with the copy-neutral call.

Author(s)

Henrik Bengtsson

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);

fit <- bootstrapTCNandDHByRegion(fit, verbose=-10);

fitC <- callCopyNeutralRegions(fit, verbose=-10);
print(fitC);

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

} # if (require("PSCBS"))

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