diff --git a/R/read-adat.R b/R/read-adat.R index 899a51c..d72ce98 100644 --- a/R/read-adat.R +++ b/R/read-adat.R @@ -131,7 +131,7 @@ read_adat <- function(file, debug = FALSE, verbose = getOption("verbose"), ...) #' Alias to `read.adat` #' #' [read.adat()] is `r lifecycle::badge("superseded")`. -#' For backward compatibility will likely never go away completely, +#' For backward compatibility it will likely never go away completely, #' but you are strongly encouraged to shift your code to use [read_adat()]. #' #' @rdname read_adat diff --git a/R/z-deprecated.R b/R/z-deprecated.R index f11de19..e63af5c 100644 --- a/R/z-deprecated.R +++ b/R/z-deprecated.R @@ -1,39 +1,40 @@ #' Deprecated function(s) of the \pkg{SomaDataIO} package #' #' @description -#' `r lifecycle::badge("superseded")` -#' +#' These functions have either been +#' `r lifecycle::badge("superseded")` or #' `r lifecycle::badge("deprecated")` -#' -#' `r lifecycle::badge("soft-deprecated")` -#' -#' These functions are provided for compatibility with -#' older versions of the \pkg{SomaDataIO} package. +#' in the current version of \pkg{SomaDataIO} package. #' They may eventually be completely removed, so #' please re-code your scripts accordingly based on the #' suggestions below: #' #' \tabular{lcr}{ -#' `meltExpressionSet()` \tab now use \tab [pivotExpressionSet()] \cr -#' `getSomamers()` \tab now use \tab [getAnalytes()] \cr -#' `getFeatures()` \tab now use \tab [getAnalytes()] \cr -#' `getSomamerData()` \tab now use \tab [getAnalyteInfo()] \cr -#' `getFeatureData()` \tab now use \tab [getAnalyteInfo()] +#' **Function** \tab \tab **Now Use** \cr +#' [getSomamers()] \tab `r lifecycle::badge("superseded")` \tab [getAnalytes()] \cr +#' [getSomamerData()] \tab `r lifecycle::badge("superseded")` \tab [getAnalyteInfo()] \cr #' } #' -#' @rdname SomaDataIO-deprecated +#' @details +#' Some badges you may see in \pkg{SomaDataIO}: +#' +#' `r lifecycle::badge("superseded")` +#' +#' `r lifecycle::badge("deprecated")` +#' +#' `r lifecycle::badge("soft-deprecated")` +#' +#' `r lifecycle::badge("stable")` +#' #' @name SomaDataIO-deprecated -#' @author Stu Field -#' @param ... A pass-through to allow the function to -#' trigger the `lifecycle` message. -#' @aliases meltExpressionSet getSomamers getSomamerData +# @inheritParams params +#' @aliases getSomamers getSomamerData #' @importFrom lifecycle deprecate_warn deprecate_stop NULL - #' @describeIn getAnalyteInfo -#' `r lifecycle::badge("superseded")`. Please adjust your code accordingly. +#' `r lifecycle::badge("superseded")`. Please now use [getAnalyteInfo()]. #' @export getFeatureData <- function(adat) { deprecate_warn("5.1.0", "SomaDataIO::getFeatureData()", "getAnalyteInfo()") @@ -41,27 +42,28 @@ getFeatureData <- function(adat) { } #' @describeIn getAnalytes -#' `r lifecycle::badge("superseded")`. Please adjust your code accordingly. +#' `r lifecycle::badge("superseded")`. Please now use [getAnalytes()]. #' @export getFeatures <- function(x, n = FALSE, rm.controls = FALSE) { deprecate_warn("5.1.0", "SomaDataIO::getFeatures()", "getAnalytes()") getAnalytes(x = x, n = n, rm.controls = rm.controls) } -#' @noRd +#' @describeIn pivotExpressionSet +#' `r lifecycle::badge("superseded")`. Please now use [pivotExpressionSet()]. #' @export -meltExpressionSet <- function(...) { +meltExpressionSet <- function(eSet) { deprecate_stop("5.0.0", "SomaDataIO::meltExpressionSet()", "pivotExpressionSet()") } #' @noRd #' @export -getSomamers <- function(...) { +getSomamers <- function(x) { deprecate_stop("5.0.0", "SomaDataIO::getSomamers()", "getAnalytes()") } #' @noRd #' @export -getSomamerData <- function(...) { +getSomamerData <- function(x) { deprecate_stop("5.0.0", "SomaDataIO::getSomamerData()", "getAnalyteInfo()") } diff --git a/man/SomaDataIO-deprecated.Rd b/man/SomaDataIO-deprecated.Rd index c22b31d..6481ac1 100644 --- a/man/SomaDataIO-deprecated.Rd +++ b/man/SomaDataIO-deprecated.Rd @@ -2,35 +2,32 @@ % Please edit documentation in R/z-deprecated.R \name{SomaDataIO-deprecated} \alias{SomaDataIO-deprecated} -\alias{meltExpressionSet} \alias{getSomamers} \alias{getSomamerData} \title{Deprecated function(s) of the \pkg{SomaDataIO} package} -\arguments{ -\item{...}{A pass-through to allow the function to -trigger the \code{lifecycle} message.} -} \description{ -\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#superseded}{\figure{lifecycle-superseded.svg}{options: alt='[Superseded]'}}}{\strong{[Superseded]}} - +These functions have either been +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#superseded}{\figure{lifecycle-superseded.svg}{options: alt='[Superseded]'}}}{\strong{[Superseded]}} or \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} - -\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#soft-deprecated}{\figure{lifecycle-soft-deprecated.svg}{options: alt='[Soft-deprecated]'}}}{\strong{[Soft-deprecated]}} - -These functions are provided for compatibility with -older versions of the \pkg{SomaDataIO} package. +in the current version of \pkg{SomaDataIO} package. They may eventually be completely removed, so please re-code your scripts accordingly based on the suggestions below: \tabular{lcr}{ -\code{meltExpressionSet()} \tab now use \tab \code{\link[=pivotExpressionSet]{pivotExpressionSet()}} \cr -\code{getSomamers()} \tab now use \tab \code{\link[=getAnalytes]{getAnalytes()}} \cr -\code{getFeatures()} \tab now use \tab \code{\link[=getAnalytes]{getAnalytes()}} \cr -\code{getSomamerData()} \tab now use \tab \code{\link[=getAnalyteInfo]{getAnalyteInfo()}} \cr -\code{getFeatureData()} \tab now use \tab \code{\link[=getAnalyteInfo]{getAnalyteInfo()}} +\strong{Function} \tab \tab \strong{Now Use} \cr +\code{\link[=getSomamers]{getSomamers()}} \tab \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#superseded}{\figure{lifecycle-superseded.svg}{options: alt='[Superseded]'}}}{\strong{[Superseded]}} \tab \code{\link[=getAnalytes]{getAnalytes()}} \cr +\code{\link[=getSomamerData]{getSomamerData()}} \tab \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#superseded}{\figure{lifecycle-superseded.svg}{options: alt='[Superseded]'}}}{\strong{[Superseded]}} \tab \code{\link[=getAnalyteInfo]{getAnalyteInfo()}} \cr } } -\author{ -Stu Field +\details{ +Some badges you may see in \pkg{SomaDataIO}: + +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#superseded}{\figure{lifecycle-superseded.svg}{options: alt='[Superseded]'}}}{\strong{[Superseded]}} + +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} + +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#soft-deprecated}{\figure{lifecycle-soft-deprecated.svg}{options: alt='[Soft-deprecated]'}}}{\strong{[Soft-deprecated]}} + +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}} } diff --git a/man/getAnalyteInfo.Rd b/man/getAnalyteInfo.Rd index 04efcd2..43d63a9 100644 --- a/man/getAnalyteInfo.Rd +++ b/man/getAnalyteInfo.Rd @@ -44,7 +44,7 @@ to its corresponding \code{TargetName} in \code{tbl}. This structure which provides a convenient auto-completion mechanism at the command line or for generating plot titles. -\item \code{getFeatureData()}: \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#superseded}{\figure{lifecycle-superseded.svg}{options: alt='[Superseded]'}}}{\strong{[Superseded]}}. Please adjust your code accordingly. +\item \code{getFeatureData()}: \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#superseded}{\figure{lifecycle-superseded.svg}{options: alt='[Superseded]'}}}{\strong{[Superseded]}}. Please now use \code{\link[=getAnalyteInfo]{getAnalyteInfo()}}. }} \examples{ diff --git a/man/getAnalytes.Rd b/man/getAnalytes.Rd index ddb1e3e..705c633 100644 --- a/man/getAnalytes.Rd +++ b/man/getAnalytes.Rd @@ -53,7 +53,7 @@ S3 methods exist for these classes: } \section{Functions}{ \itemize{ -\item \code{getFeatures()}: \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#superseded}{\figure{lifecycle-superseded.svg}{options: alt='[Superseded]'}}}{\strong{[Superseded]}}. Please adjust your code accordingly. +\item \code{getFeatures()}: \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#superseded}{\figure{lifecycle-superseded.svg}{options: alt='[Superseded]'}}}{\strong{[Superseded]}}. Please now use \code{\link[=getAnalytes]{getAnalytes()}}. }} \examples{ diff --git a/man/pivotExpressionSet.Rd b/man/pivotExpressionSet.Rd index 87806a9..d2c5a22 100644 --- a/man/pivotExpressionSet.Rd +++ b/man/pivotExpressionSet.Rd @@ -1,10 +1,13 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/pivotExpressionSet.R +% Please edit documentation in R/pivotExpressionSet.R, R/z-deprecated.R \name{pivotExpressionSet} \alias{pivotExpressionSet} +\alias{meltExpressionSet} \title{Convert to Long Format} \usage{ pivotExpressionSet(eSet) + +meltExpressionSet(eSet) } \arguments{ \item{eSet}{An \code{ExpressionSet} class object, created using \code{\link[=adat2eSet]{adat2eSet()}}.} @@ -18,6 +21,11 @@ Utility to convert an \code{ExpressionSet} class object from the "wide" data format to the "long" format via \code{\link[=pivot_longer]{pivot_longer()}}. The \pkg{Biobase} package is required for this function. } +\section{Functions}{ +\itemize{ +\item \code{meltExpressionSet()}: \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#superseded}{\figure{lifecycle-superseded.svg}{options: alt='[Superseded]'}}}{\strong{[Superseded]}}. Please now use \code{\link[=pivotExpressionSet]{pivotExpressionSet()}}. + +}} \examples{ # subset into a reduced mini-ADAT object # 10 samples (rows) diff --git a/man/read_adat.Rd b/man/read_adat.Rd index 1eb7cda..7369b2b 100644 --- a/man/read_adat.Rd +++ b/man/read_adat.Rd @@ -44,7 +44,7 @@ an R workspace environment. The class of the returned object is a \code{soma_adat} object. \code{\link[=read.adat]{read.adat()}} is \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#superseded}{\figure{lifecycle-superseded.svg}{options: alt='[Superseded]'}}}{\strong{[Superseded]}}. -For backward compatibility will likely never go away completely, +For backward compatibility it will likely never go away completely, but you are strongly encouraged to shift your code to use \code{\link[=read_adat]{read_adat()}}. \code{\link[=is.soma_adat]{is.soma_adat()}} checks whether an object is of class \code{soma_adat}.