Nothing
###########################################################################/**
# @RdocClass AromaUnitPscnBinaryFile
#
# @title "The AromaUnitPscnBinaryFile class"
#
# \description{
# @classhierarchy
#
# An AromaUnitPscnBinaryFile is a @see "AromaUnitSignalBinaryFile"
# that holds total copy number signals (TCNs) and allele B fractions (BAFs).
# The TCNs can either be on an unknown scale or ratios relative
# to a reference. The signals are always stored on the original scale,
# i.e. they are never stored on the logaritmic scale.
# The BAFs are always on a [0-eps,1+eps] scale, where eps >= 0.
# }
#
# @synopsis
#
# \arguments{
# \item{...}{Arguments passed to @see "AromaUnitSignalBinaryFile".}
# }
#
# \section{Fields and Methods}{
# @allmethods "public"
# }
#
# @author
#*/###########################################################################
setConstructorS3("AromaUnitPscnBinaryFile", function(...) {
extend(AromaUnitSignalBinaryFile(...), c("AromaUnitPscnBinaryFile", uses("CopyNumberDataFile"))
)
})
setMethodS3("hasTotalCopyNumberRatios", "AromaUnitPscnBinaryFile", function(this, ...) {
hasTag(this, "ratio")
})
setMethodS3("hasAlleleBFractions", "AromaUnitPscnBinaryFile", function(this, ...) {
# By definition, always TRUE
TRUE
})
setMethodS3("hasStrandiness", "AromaUnitPscnBinaryFile", function(this, ...) {
# For now always FALSE, due to how the (super)classes are defined.
# /HB 2009-11-19
FALSE
})
setMethodS3("getDefaultColumnNames", "AromaUnitPscnBinaryFile", function(this, ...) {
.stop_if_not(nbrOfColumns(this) == 2L)
c("total", "fracB")
}, protected=TRUE)
setMethodS3("extractRawCopyNumbers", "AromaUnitPscnBinaryFile", function(this, ..., logBase=2L, clazz=RawCopyNumbers) {
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Validate arguments
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Argument 'logBase':
if (!is.null(logBase)) {
logBase <- Arguments$getDouble(logBase, range=c(1, 10))
}
# Total CN signals are always stored on the original scale in column #1.
cn <- extractRawGenomicSignals(this, column=1L, ..., clazz=clazz)
# Convert to the correct logarithmic base
cn <- extractRawCopyNumbers(cn, logBase=logBase)
cn
})
setMethodS3("allocate", "AromaUnitPscnBinaryFile", function(static, ..., platform, chipType, types=c("double", "double"), sizes=c(4L, 4L), signed=c(TRUE, TRUE), footer=list()) {
# Argument 'platform':
platform <- Arguments$getCharacter(platform, length=c(1,1))
# Argument 'chipType':
chipType <- Arguments$getCharacter(chipType, length=c(1,1))
# Create tabular binary file
res <- NextMethod("allocate", generic="allocate", types=types, sizes=sizes, signeds=signed)
# Write attributes to footer
attrs <- list(
createdOn=format(Sys.time(), "%Y%m%d %H:%M:%S", usetz=TRUE),
platform=platform,
chipType=chipType
)
footer <- c(attrs, footer)
writeFooter(res, footer)
res
}, static=TRUE, protected=TRUE)
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