diff --git a/DESCRIPTION b/DESCRIPTION index d40fdcb..1b21b5e 100644 --- a/DESCRIPTION +++ b/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 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 diff --git a/vignettes/SummarizedExperiment.Rmd b/vignettes/SummarizedExperiment.Rmd new file mode 100644 index 0000000..cf06123 --- /dev/null +++ b/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_ \ No newline at end of file