###########################################################################/**
# @RdocClass AromaUnitTotalCnBinaryFile
#
# @title "The AromaUnitTotalCnBinaryFile class"
#
# \description{
# @classhierarchy
#
# An AromaUnitTotalCnBinaryFile is a @see "AromaUnitSignalBinaryFile".
# }
#
# @synopsis
#
# \arguments{
# \item{...}{Arguments passed to @see "AromaUnitSignalBinaryFile".}
# }
#
# \section{Fields and Methods}{
# @allmethods "public"
# }
#
# @author
#*/###########################################################################
setConstructorS3("AromaUnitTotalCnBinaryFile", function(...) {
extend(AromaUnitSignalBinaryFile(...), c("AromaUnitTotalCnBinaryFile", uses("CopyNumberDataFile"))
)
})
setMethodS3("hasAlleleBFractions", "AromaUnitTotalCnBinaryFile", function(this, ...) {
# By definition, always FALSE
FALSE
})
setMethodS3("hasStrandiness", "AromaUnitTotalCnBinaryFile", function(this, ...) {
# For now always FALSE, due to how the (super)classes are defined.
# /HB 2009-11-19
FALSE
})
setMethodS3("extractRawCopyNumbers", "AromaUnitTotalCnBinaryFile", function(this, ..., logBase=2, clazz=RawCopyNumbers) {
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Validate arguments
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Argument 'logBase':
if (!is.null(logBase)) {
logBase <- Arguments$getDouble(logBase, range=c(1, 10))
}
cn <- extractRawGenomicSignals(this, ..., clazz=clazz)
logBase0 <- NULL
if (hasTag(this, "log2ratio")) {
logBase0 <- 2
} else if (hasTag(this, "log10ratio")) {
logBase0 <- 10
} else if (hasTag(this, "logRatio")) {
# AD HOC. Now standard
logBase0 <- 10
}
cn <- setBasicField(cn, ".yLogBase", logBase0)
# Convert to the correct logarithmic base
cn <- extractRawCopyNumbers(cn, logBase=logBase)
cn
})
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