Move documentation and unit tests for makeSummarizedExperimentFromExp…

…ressionSet

and related stuff to the new SummarizedExperiment package.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@103877 bc3139a8-67e5-0310-9ffc-ced21a209358

R/SummarizedExperiment-class.R

@@ -834,7 +834,7 @@ setMethod(show, "SummarizedExperiment",
     scat("colData names(%d): %s\n", names(colData(object)))
 })
 
-## compatibility
+## transition to RangedSummarizedExperiment
 
 suppressMessages(
   setAs("SummarizedExperiment", "RangedSummarizedExperiment",

man/SummarizedExperiment-class.Rd

@@ -15,12 +15,6 @@
 \alias{SummarizedExperiment,list-method}
 \alias{SummarizedExperiment,SimpleList-method}
 
-% Coercion methods:
-\alias{coerce,ExpressionSet,SummarizedExperiment-method}
-\alias{coerce,SummarizedExperiment,ExpressionSet-method}
-\alias{coerce,SummarizedExperiment,RangedSummarizedExperiment-method}
-\alias{updateObject,SummarizedExperiment-method}
-
 % Accessor methods:
 \alias{assays}
 \alias{assays,SummarizedExperiment-method}
@@ -145,6 +139,12 @@
 % show method:
 \alias{show,SummarizedExperiment-method}
 
+% transition to RangedSummarizedExperiment:
+\alias{coerce,SummarizedExperiment,RangedSummarizedExperiment-method}
+\alias{updateObject,SummarizedExperiment-method}
+\alias{coerce,SummarizedExperiment,ExpressionSet-method}
+\alias{coerce,ExpressionSet,SummarizedExperiment-method}
+
 \title{SummarizedExperiment instances}
 
 \description{
@@ -153,7 +153,7 @@
   replaced with the \link[SummarizedExperiment]{RangedSummarizedExperiment}
   class defined in the new \pkg{SummarizedExperiment} package.
   Please make sure to install the \pkg{SummarizedExperiment} package before
-  you attempt to call the \code{SummarizedExperiment()} constructor function.
+  you attempt to use the \code{SummarizedExperiment()} constructor function.
   Note that this will return a
   \link[SummarizedExperiment]{RangedSummarizedExperiment} instance instead
   of a SummarizedExperiment instance. 

man/makeSummarizedExperimentFromExpressionSet.Rd

@@ -2,53 +2,17 @@
 
 \alias{makeSummarizedExperimentFromExpressionSet}
 
-\title{Make an SummarizedExperiment object from an ExpressionSet}
+\title{Make a SummarizedExperiment object from an ExpressionSet}
 
 \description{
-  \code{makeSummarizedExperimentFromExpressionSet} takes a
-  \link[Biobase]{ExpressionSet} object as input and a Range mapping function
-  that maps the features to ranges.  It then returns a
-  \link{SummarizedExperiment} object.
+  WARNING: The SummarizedExperiment class is deprecated and being
+  replaced with the \link[SummarizedExperiment]{RangedSummarizedExperiment}
+  class defined in the new \pkg{SummarizedExperiment} package.
+
+  Please make sure to install and load the \pkg{SummarizedExperiment} package
+  where the \code{makeSummarizedExperimentFromExpressionSet} function is now
+  defined and documented. Note that the function now returns a
+  \link[SummarizedExperiment]{RangedSummarizedExperiment} instance instead
+  of a \link{SummarizedExperiment} instance.
 }
 
-\usage{
-makeSummarizedExperimentFromExpressionSet(from,
-                                          mapFun=naiveRangeMapper)
-}
-
-\arguments{
-  \item{from}{
-    An \link[Biobase]{ExpressionSet} object.
-  }
-  \item{mapFun}{
-    A function which takes an \link[Biobase]{ExpressionSet} object and
-    returns a \link{GRanges}, or \link{GRangesList} object which
-    corresponds to the genomic ranges used in the ExpressionSet.  The
-    \link[base]{rownames} of the returned \link{GRanges} are used to match the
-    \link[Biobase]{featureNames} of the \link[Biobase]{ExpressionSet}.
-    \link{naiveRangeMapper}.
-  }
-}
-
-\value{
-  A \link{SummarizedExperiment} object that corresponds to the input.
-}
-
-\seealso{
-  \link{naiveRangeMapper}, \link{probeRangeMapper}, \link{geneRangeMapper}
-}
-\examples{
-
-  library(Biobase)
-  data(sample.ExpressionSet, package = "Biobase")
-
-  # using the naive coercion
-  makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet)
-
-  # using probe range mapper
-  makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet, probeRangeMapper)
-
-  # using the gene range mapper
-  makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet,
-                                            geneRangeMapper("TxDb.Hsapiens.UCSC.hg19.knownGene"))
-}