Nothing
###########################################################################/**
# @RdocClass RawCopyNumbers
#
# @title "The RawCopyNumbers class"
#
# \description{
# @classhierarchy
# }
#
# @synopsis
#
# \arguments{
# \item{cn}{A @numeric @vector of length J specifying the copy number
# at each loci.}
# \item{...}{Arguments passed to @see "RawGenomicSignals".}
# }
#
# \section{Fields and Methods}{
# @allmethods "public"
# }
#
# @examples "../incl/RawCopyNumbers.Rex"
#
# @author
#*/###########################################################################
setConstructorS3("RawCopyNumbers", function(cn=NULL, ...) {
this <- extend(RawGenomicSignals(y=cn, ...), "RawCopyNumbers")
this <- setColumnNamesMap(this, y="cn")
this
})
setMethodS3("getSignals", "RawCopyNumbers", function(this, ...) {
this$cn
})
setMethodS3("getCNs", "RawCopyNumbers", function(this, ...) {
getSignals(this)
}, protected=TRUE)
setMethodS3("getCn", "RawCopyNumbers", function(this, ...) {
getSignals(this)
}, protected=TRUE)
setMethodS3("extractRawCopyNumbers", "RawCopyNumbers", function(this, ..., logBase=2) {
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Validate arguments
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Argument 'logBase':
if (!is.null(logBase)) {
logBase <- Arguments$getDouble(logBase, range=c(1, 10))
}
# Get the current logarithmic base, if any
logBase0 <- getBasicField(this, ".yLogBase")
res <- clone(this)
if (!isTRUE(all.equal(logBase0, logBase))) {
# Get current signals
y <- getSignals(this)
# Unlog?
if (!is.null(logBase0)) {
y <- logBase0^y
}
# Log?
if (!is.null(logBase)) {
y <- log(y) / log(logBase)
}
res <- setSignals(res, y)
res <- setBasicField(res, ".yLogBase", logBase)
}
res
})
setMethodS3("plot", "RawCopyNumbers", function(x, ..., ylim=c(0,5), ylab="Copy number") {
NextMethod("plot", ylim=ylim, ylab=ylab)
})
setMethodS3("cnRange", "RawCopyNumbers", function(this, ...) {
signalRange(this, ...)
})
setMethodS3("extractRawCNs", "default", function(...) {
extractRawCopyNumbers(...)
})
setMethodS3("extractRawCopyNumbers", "default", abstract=TRUE)
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