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aroma.cn (version 1.6.1)

callCopyNeutralRegions.PairedPSCBS: Calls regions that are copy neutral

Description

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

Usage

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

Value

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

Arguments

fit

A PairedPSCBS fit object as returned by segmentByPairedPSCBS.

...

Additional arguments passed to callCopyNeutral.PairedPSCBS.

Author

Henrik Bengtsson

Examples

Run this code

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"))

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