tests/callAllelicBalanceByBAFs.PairedPSCBS.R

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

library("aroma.cn")
options("PSCBS/preserveScale"=FALSE)

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"))