add vignette stub

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SummarizedExperiment@103829 bc3139a8-67e5-0310-9ffc-ced21a209358

DESCRIPTION

@@ -4,13 +4,15 @@ Description: The SummarizedExperiment container contains one or more assays,
 	each represented by a matrix-like object of numeric or other mode.
 	The rows typically represent genomic ranges of interest and the columns
 	represent samples.
-Version: 0.1.3
+Version: 0.1.4
 Author: Martin Morgan, Valerie Obenchain, Jim Hester, Herv\'e Pag\`es
 Maintainer: Bioconductor Package Maintainer <[email protected]>
 biocViews: Genetics, Infrastructure, Sequencing, Annotation, Coverage,
 	GenomeAnnotation
 Depends: R (>= 3.2), methods, GenomicRanges (>= 1.21.8)
 Imports: BiocGenerics, S4Vectors, IRanges, GenomeInfoDb
+Suggests: BiocStyle, knitr, rmarkdown
+VignetteBuilder: knitr
 License: Artistic-2.0
 Collate: SummarizedExperiment-class.R
 	SummarizedExperiment-rowRanges-methods.R

vignettes/SummarizedExperiment.Rmd

@@ -0,0 +1,34 @@
+---
+title: "_SummarizedExperiment_ for Coordinating Experimental Assays, Samples, and Regions of Interest"
+author: "Martin Morgan"
+date: "Revised: 14 May, 2015"
+output:
+  BiocStyle::html_document:
+    toc: true
+vignette: >
+  %\VignetteIndexEntry{SummarizedExperiment}
+  %\VignetteEngine{knitr::rmarkdown}
+  \usepackage[utf8]{inputenc}
+---
+
+```{r style, echo=FALSE, results='asis'}
+BiocStyle::markdown()
+```
+
+# Motivating use case
+
+# Parts of a _SummarizedExperiment_
+
+## Assays
+
+## 'Row' (regions-of-interest) data
+
+### Genomic ranges or data frames?
+
+## Experimental metadata
+
+# Common operations on _SummarizedExperiment_
+
+# Case study revisited -- _SummarizedExperiment_ in action
+
+# Advanced: Extending _SummarizedExperiment_