callAllelicBalanceByBAFs.PairedPSCBS: Calls regions that are in allelic balance

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

Calls regions that are in allelic balance

Description

Calls regions that are in allelic balance from the allele B fractions (BAF).

Usage

## S3 method for class 'PairedPSCBS'
callAllelicBalanceByBAFs(fit, maxScore="auto", ..., force=FALSE, cache=FALSE,
  verbose=FALSE)

Arguments

fit	A PairedPSCBS fit object as returned by segmentByPairedPSCBS.
maxScore	A positive double threshold. If "auto", the threshold is estimated empirically.
...	Not used.
force	If TRUE, an already called object is skipped, otherwise not.
verbose	See Verbose.

Value

Returns a PairedPSCBS fit object where columns for allelic imbalance scores and p-values as well as allelic balance calls are added.

Author(s)

Henrik Bengtsson, Pierre Neuvial

See Also

Internally, testAllelicBalanceByBAFs() is used.

Note that this AB caller differs from the default one in the PSCBS package, cf. callAB.PairedPSCBS.

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.