---
title: "H. Integrative Analysis"
author: Martin Morgan (mtmorgan@fredhutch.org)
date: "`r Sys.Date()`"
output:
  BiocStyle::html_document:
    toc: true
vignette: >
  %\VignetteIndexEntry{H. Integrative Analysis}
  %\VignetteEngine{knitr::rmarkdown}
  \usepackage[utf8]{inputenc}
---

```{r style, echo=FALSE, results='asis'}
BiocStyle::markdown()
```

# Scope and opportunity

## Case study 1: TCGA Copy Number / Expression

# Accessing 'Consortium' data

# Representing integrated data sets

## Key components

Samples

- Including 'phenotypic' attributes measured on each

Assays

- Often, rectangular features x samples `matrix()` of values
- A different representation: `data.frame()` of feature, sample, value
  tuples.

Experiments

- Sample inputs to each experiment
- Assay outputs from each experiment
- Additional experiment-specific information, each date on which
  samples were processed
  
## Alternative Representations

R-based representations

Other approaches

- Data base
- 'Scientific' representations, e.g.,
  [HDF5](http://www.hdfgroup.org/HDF5/)
- 'Computational' representations, e.g.,
  [HDFS](http://hadoop.apache.org/docs/r1.2.1/hdfs_design.html)

## A preliminary design

# Statistical and other challenges

# Practical
