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Rd: fix up help pages, e.g. cleaning up arguments that are documented…
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… that shouldn't be documented
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HenrikBengtsson committed Feb 18, 2024
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2 changes: 1 addition & 1 deletion DESCRIPTION
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@@ -1,5 +1,5 @@
Package: aroma.affymetrix
Version: 3.2.1-9002
Version: 3.2.1-9003
Depends:
R (>= 3.2.0),
R.utils (>= 2.9.0),
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2 changes: 0 additions & 2 deletions R/AffymetrixCdfFile.R
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Expand Up @@ -420,7 +420,6 @@ setMethodS3("hasUnitTypes", "AffymetrixCdfFile", function(this, types, ..., verb
#
# \arguments{
# \item{units}{The units of interest. If @NULL, all units are considered.}
# \item{map}{A @character string specifying the mapping used.}
# \item{...}{Not used.}
# }
#
Expand Down Expand Up @@ -834,7 +833,6 @@ setMethodS3("restruct", "AffymetrixCdfFile", function(this, cdf, ..., verbose=FA
# @synopsis
#
# \arguments{
# \item{units}{The units of interest. If @NULL, all units are considered.}
# \item{...}{Additional arguments passed to
# @see "affxparser::readCdfCellIndices".}
# }
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5 changes: 2 additions & 3 deletions R/AffymetrixCelFile.PLOT.R
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Expand Up @@ -313,8 +313,8 @@ setMethodS3("smoothScatterMvsA", "AffymetrixCelFile", function(this, reference,
# \item{x}{The other variable. A @double @vector.}
# \item{indices}{Indices of the probe signals to be plotted.}
# \item{pch}{The plot symbol.}
# \item{xlim,ylim}{The range of the x and the y axes.}
# \item{xlab,ylab}{The labels on the x and the y axes.}
# \item{ylim}{The range of the y axes.}
# \item{ylab}{The labels on the y axes.}
# \item{...}{Additional arguments passed to @see "graphics::plot".}
# \item{annotate}{If @TRUE, the plot is annotated with information about
# the data plotted, otherwise not.}
Expand Down Expand Up @@ -495,7 +495,6 @@ setMethodS3("image270", "AffymetrixCelFile", function(this, xrange=c(0,Inf), yra
# \code{stdvs}, or \code{pixels}.}
# \item{zoom}{A @numeric scale factor in (0,+Inf) for resizing the
# imaging. If \code{1}, no resizing is done.}
# \item{palette}{An optional @vector of color code.}
# \item{...}{Additional arguments passed to
# @seemethod "readRawDataRectangle" and more function.}
# \item{readRectFcn}{A @function taking arguments 'xrange' and 'yrange',
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1 change: 1 addition & 0 deletions R/AffymetrixCelSet.R
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@@ -1,5 +1,6 @@
###########################################################################/**
# @RdocClass AffymetrixCelSet
# @alias nbrOfArrays.AffymetrixCelSet
#
# @title "The AffymetrixCelSet class"
#
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2 changes: 0 additions & 2 deletions R/AromaChipTypeAnnotationFile.R
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Expand Up @@ -229,8 +229,6 @@ setMethodS3("getDefaultExtension", "AromaChipTypeAnnotationFile", function(stati
# @synopsis
#
# \arguments{
# \item{chipType}{A @character string.}
# \item{tags}{An optional @character @vector of tags.}
# \item{...}{Additional arguments.}
# }
#
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5 changes: 0 additions & 5 deletions R/AromaUnitTabularBinaryFile.AFFX.R
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Expand Up @@ -86,11 +86,6 @@ setMethodS3("getCdf", "AromaUnitTabularBinaryFile", function(this, ..., force=FA
# \arguments{
# \item{cdf}{The @see "AffymetrixCdfFile" used as a template and from
# which the (full) chip type is taken.}
# \item{path}{The path where to store the new file.}
# \item{tags}{A @character @vector of optional tags appended to
# the filename.}
# \item{footer}{A nested named @list structure of additional attributes
# that are saved in the file footer after the mandatory ones.}
# \item{...}{Additional arguments passed to \code{allocate()} of
# @see "aroma.core::AromaTabularBinaryFile".}
# }
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2 changes: 0 additions & 2 deletions R/ArrayExplorer.R
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Expand Up @@ -180,8 +180,6 @@ setMethodS3("getArraysOfInput", "ArrayExplorer", function(this, ...) {
# @synopsis
#
# \arguments{
# \item{arrays}{A @character (or @integer) @vector of arrays to be
# considered. If @NULL, all arrays of the data set are considered.}
# \item{...}{Not used.}
# }
#
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3 changes: 0 additions & 3 deletions R/BackgroundCorrection.R
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Expand Up @@ -69,9 +69,6 @@ setMethodS3("getParameters", "BackgroundCorrection", function(this, ...) {
#
# \arguments{
# \item{...}{Not used.}
# \item{force}{If @TRUE, data already processed is re-processed,
# otherwise not.}
# \item{verbose}{See @see "R.utils::Verbose".}
# }
#
# \value{
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2 changes: 0 additions & 2 deletions R/CnagCfhFile.R
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Expand Up @@ -356,8 +356,6 @@ setMethodS3("getChipType", "CnagCfhFile", function(this, ...) {
#
# \arguments{
# \item{units}{The units to be read. If @NULL, all units are read.}
# \item{cdf}{An alternative CDF structure to be used. This overrides
# the \code{units} arguments.}
# \item{...}{Arguments passed to \code{getUnits()} of the
# @see "AffymetrixCdfFile" class (if \code{cdf} was not specified),
# but also to the @see "affxparser::readCelUnits" methods.}
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7 changes: 1 addition & 6 deletions R/DChipSnpInformation.R
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Expand Up @@ -94,14 +94,9 @@ setMethodS3("findByChipType", "DChipSnpInformation", function(static, chipType,
#
# \arguments{
# \item{chipType}{A @character string.}
# \item{rootPath}{A @character string specifying the root path, i.e.
# the annotation directory.}
# \item{version}{An optional @character string specifying the version
# string, if more than one version is available.}
# \item{pattern}{An optional filename pattern used to locate the
# dChip genome file. If @NULL, a default pattern is used.}
# \item{...}{Not used.}
# \item{verbose}{See @see "R.utils::Verbose".}
# \item{...}{Additional arguments passed to @seemethod "findByChipType".}
# }
#
# \value{
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2 changes: 0 additions & 2 deletions R/ExonChipEffectFile.R
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Expand Up @@ -59,8 +59,6 @@ setMethodS3("getParameters", "ExonChipEffectFile", function(this, ...) {
# @synopsis
#
# \arguments{
# \item{units}{Unit indices to be retrieved.
# If @NULL, all units are considered.}
# \item{...}{Additional arguments passed to \code{getCellIndices()}
# of @see "ChipEffectFile".}
# \item{unlist}{If @TRUE, the cell indices are returned as a @vector.}
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1 change: 0 additions & 1 deletion R/FirmaModel.R
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Expand Up @@ -263,7 +263,6 @@ setMethodS3("getFirmaScores", "FirmaModel", function(this, ...) {
#
# \arguments{
# \item{...}{Not used.}
# \item{verbose}{A @logical or a @see "R.utils::Verbose".}
# }
#
# \value{
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3 changes: 0 additions & 3 deletions R/SmoothMultiarrayModel.fit.R
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Expand Up @@ -14,9 +14,6 @@ setMethodS3("getFitUnitGroupFunction", "SmoothMultiarrayModel", abstract=TRUE, p
# @synopsis
#
# \arguments{
# \item{data}{A @data.frame with columns \code{M} (log-ratio) and
# \code{x} (locus position).
# }
# \item{chromosome}{An @integer specifying the index of the chromosome to
# be fitted.}
# \item{...}{Additional arguments passed down to the internal fit function.}
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1 change: 0 additions & 1 deletion R/Transform.R
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Expand Up @@ -31,7 +31,6 @@ setMethodS3("getOutputFiles", "Transform", function(this, pattern=NULL, ...) {
#
# \arguments{
# \item{...}{Not used.}
# \item{force}{If @TRUE, any in-memory cached results are ignored.}
# \item{verbose}{See @see "R.utils::Verbose".}
# }
#
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4 changes: 1 addition & 3 deletions R/UgpGenomeInformation.R
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Expand Up @@ -68,9 +68,7 @@ setMethodS3("findByChipType", "UgpGenomeInformation", function(static, ...) {
# \arguments{
# \item{chipType}{A @character string.}
# \item{tags}{...}
# \item{version}{An optional @character string specifying the version
# string, if more than one version is available.}
# \item{...}{Not used.}
# \item{...}{Additional arguments passed to @see "UgpGenomeInformation".}
# \item{verbose}{See @see "R.utils::Verbose".}
# }
#
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1 change: 1 addition & 0 deletions R/setupExampleData.R
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@@ -1,6 +1,7 @@
###########################################################################/**
# @set class=AromaAffymetrix
# @RdocMethod setupExampleData
# @alias setupExampleData
#
# @title "Setups example data in the current directory"
#
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1 change: 1 addition & 0 deletions man/AffymetrixCelSet.Rd
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Expand Up @@ -10,6 +10,7 @@
\docType{class}
\alias{AffymetrixCelSet}

\alias{nbrOfArrays.AffymetrixCelSet}

\title{The AffymetrixCelSet class}

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5 changes: 0 additions & 5 deletions man/allocateFromCdf.AromaUnitTabularBinaryFile.Rd
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Expand Up @@ -30,11 +30,6 @@
\arguments{
\item{cdf}{The \code{\link{AffymetrixCdfFile}} used as a template and from
which the (full) chip type is taken.}
\item{path}{The path where to store the new file.}
\item{tags}{A \code{\link[base]{character}} \code{\link[base]{vector}} of optional tags appended to
the filename.}
\item{footer}{A nested named \code{\link[base]{list}} structure of additional attributes
that are saved in the file footer after the mandatory ones.}
\item{...}{Additional arguments passed to \code{allocate()} of
\code{\link[aroma.core]{AromaTabularBinaryFile}}.}
}
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7 changes: 1 addition & 6 deletions man/byChipType.DChipSnpInformation.Rd
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Expand Up @@ -23,14 +23,9 @@

\arguments{
\item{chipType}{A \code{\link[base]{character}} string.}
\item{rootPath}{A \code{\link[base]{character}} string specifying the root path, i.e.
the annotation directory.}
\item{version}{An optional \code{\link[base]{character}} string specifying the version
string, if more than one version is available.}
\item{pattern}{An optional filename pattern used to locate the
dChip genome file. If \code{\link[base]{NULL}}, a default pattern is used.}
\item{...}{Not used.}
\item{verbose}{See \code{\link[R.utils]{Verbose}}.}
\item{...}{Additional arguments passed to \code{\link[aroma.affymetrix:findByChipType.DChipSnpInformation]{*findByChipType}()}.}
}

\value{
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4 changes: 1 addition & 3 deletions man/byChipType.UgpGenomeInformation.Rd
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Expand Up @@ -30,9 +30,7 @@
\arguments{
\item{chipType}{A \code{\link[base]{character}} string.}
\item{tags}{...}
\item{version}{An optional \code{\link[base]{character}} string specifying the version
string, if more than one version is available.}
\item{...}{Not used.}
\item{...}{Additional arguments passed to \code{\link{UgpGenomeInformation}}.}
\item{verbose}{See \code{\link[R.utils]{Verbose}}.}
}

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1 change: 0 additions & 1 deletion man/calculateResidualSet.FirmaModel.Rd
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Expand Up @@ -27,7 +27,6 @@

\arguments{
\item{...}{Not used.}
\item{verbose}{A \code{\link[base]{logical}} or a \code{\link[R.utils]{Verbose}}.}
}

\value{
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2 changes: 0 additions & 2 deletions man/findByChipType.AromaChipTypeAnnotationFile.Rd
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Expand Up @@ -22,8 +22,6 @@
}

\arguments{
\item{chipType}{A \code{\link[base]{character}} string.}
\item{tags}{An optional \code{\link[base]{character}} \code{\link[base]{vector}} of tags.}
\item{...}{Additional arguments.}
}

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3 changes: 0 additions & 3 deletions man/fit.SmoothMultiarrayModel.Rd
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Expand Up @@ -23,9 +23,6 @@
}

\arguments{
\item{data}{A \code{\link[base]{data.frame}} with columns \code{M} (log-ratio) and
\code{x} (locus position).
}
\item{chromosome}{An \code{\link[base]{integer}} specifying the index of the chromosome to
be fitted.}
\item{...}{Additional arguments passed down to the internal fit function.}
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2 changes: 0 additions & 2 deletions man/getCellIndices.ExonChipEffectFile.Rd
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Expand Up @@ -22,8 +22,6 @@
}

\arguments{
\item{units}{Unit indices to be retrieved.
If \code{\link[base]{NULL}}, all units are considered.}
\item{...}{Additional arguments passed to \code{getCellIndices()}
of \code{\link{ChipEffectFile}}.}
\item{unlist}{If \code{\link[base:logical]{TRUE}}, the cell indices are returned as a \code{\link[base]{vector}}.}
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1 change: 0 additions & 1 deletion man/getImage.AffymetrixCelFile.Rd
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Expand Up @@ -35,7 +35,6 @@
\code{stdvs}, or \code{pixels}.}
\item{zoom}{A \code{\link[base]{numeric}} scale factor in (0,+Inf) for resizing the
imaging. If \code{1}, no resizing is done.}
\item{palette}{An optional \code{\link[base]{vector}} of color code.}
\item{...}{Additional arguments passed to
\code{\link[aroma.affymetrix:readRawDataRectangle.AffymetrixCelFile]{*readRawDataRectangle}()} and more function.}
\item{readRectFcn}{A \code{\link[base]{function}} taking arguments 'xrange' and 'yrange',
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1 change: 0 additions & 1 deletion man/getOutputDataSet.Transform.Rd
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Expand Up @@ -24,7 +24,6 @@

\arguments{
\item{...}{Not used.}
\item{force}{If \code{\link[base:logical]{TRUE}}, any in-memory cached results are ignored.}
\item{verbose}{See \code{\link[R.utils]{Verbose}}.}
}

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1 change: 0 additions & 1 deletion man/getUnitTypes.AffymetrixCdfFile.Rd
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Expand Up @@ -23,7 +23,6 @@

\arguments{
\item{units}{The units of interest. If \code{\link[base]{NULL}}, all units are considered.}
\item{map}{A \code{\link[base]{character}} string specifying the mapping used.}
\item{...}{Not used.}
}

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39 changes: 0 additions & 39 deletions man/nbrOfArrays.AffymetrixCelSet.Rd

This file was deleted.

4 changes: 2 additions & 2 deletions man/plotMvsX.AffymetrixCelFile.Rd
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Expand Up @@ -28,8 +28,8 @@
\item{x}{The other variable. A \code{\link[base]{double}} \code{\link[base]{vector}}.}
\item{indices}{Indices of the probe signals to be plotted.}
\item{pch}{The plot symbol.}
\item{xlim,ylim}{The range of the x and the y axes.}
\item{xlab,ylab}{The labels on the x and the y axes.}
\item{ylim}{The range of the y axes.}
\item{ylab}{The labels on the y axes.}
\item{...}{Additional arguments passed to \code{\link[graphics]{plot}}().}
\item{annotate}{If \code{\link[base:logical]{TRUE}}, the plot is annotated with information about
the data plotted, otherwise not.}
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3 changes: 0 additions & 3 deletions man/process.BackgroundCorrection.Rd
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Expand Up @@ -23,9 +23,6 @@

\arguments{
\item{...}{Not used.}
\item{force}{If \code{\link[base:logical]{TRUE}}, data already processed is re-processed,
otherwise not.}
\item{verbose}{See \code{\link[R.utils]{Verbose}}.}
}

\value{
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2 changes: 0 additions & 2 deletions man/readUnits.CnagCfhFile.Rd
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Expand Up @@ -23,8 +23,6 @@

\arguments{
\item{units}{The units to be read. If \code{\link[base]{NULL}}, all units are read.}
\item{cdf}{An alternative CDF structure to be used. This overrides
the \code{units} arguments.}
\item{...}{Arguments passed to \code{getUnits()} of the
\code{\link{AffymetrixCdfFile}} class (if \code{cdf} was not specified),
but also to the \code{\link[affxparser]{readCelUnits}} methods.}
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2 changes: 0 additions & 2 deletions man/setArrays.ArrayExplorer.Rd
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Expand Up @@ -22,8 +22,6 @@
}

\arguments{
\item{arrays}{A \code{\link[base]{character}} (or \code{\link[base]{integer}}) \code{\link[base]{vector}} of arrays to be
considered. If \code{\link[base]{NULL}}, all arrays of the data set are considered.}
\item{...}{Not used.}
}

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1 change: 0 additions & 1 deletion man/setRestructor.AffymetrixCdfFile.Rd
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Expand Up @@ -22,7 +22,6 @@
}

\arguments{
\item{units}{The units of interest. If \code{\link[base]{NULL}}, all units are considered.}
\item{...}{Additional arguments passed to
\code{\link[affxparser]{readCdfCellIndices}}.}
}
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1 change: 1 addition & 0 deletions man/setupExampleData.AromaAffymetrix.Rd
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Expand Up @@ -11,6 +11,7 @@
\alias{setupExampleData.AromaAffymetrix}
\alias{AromaAffymetrix.setupExampleData}
\alias{setupExampleData,AromaAffymetrix-method}
\alias{setupExampleData}

\title{Setups example data in the current directory}

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