---
title: "Integrative analysis workshop with TCGAbiolinks and ELMER - Get DATA GUI"
author: "Tiago Chedraoui Silva, Simon Coetzee, Dennis Hazelett, Ben Berman, Houtan Noushmehr"
date: "`r Sys.Date()`"
output: 
  html_document:
    self_contained: true
    number_sections: no
    theme: flatly
    highlight: tango
    mathjax: null
    toc: true
    toc_float: true
    toc_depth: 2
    css: style.css
bibliography: bibliography.bib    
vignette: >
  %\VignetteIndexEntry{Integrative analysis workshop with TCGAbiolinks and ELMER - Get DATA GUI}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, echo = FALSE,hide=TRUE, message=FALSE,warning=FALSE}
devtools::load_all(".")
```

# Introduction

In this section, we will download the same data using TCGAbiolinks,
but instead of doing it programmatically we will use TCGAbiolinksGUI [@Silva147496].

First we will launch the TCGAbiolinksGUI.
```{r gui, eval=FALSE, message=FALSE,warning=F}
library(TCGAbiolinksGUI)
TCGAbiolinksGUI()
```


# Downloading data 

## Gene expression

<div class="panel panel-info">
<div class="panel-body">
After launching the GUI select the `GDC Data/Get GDC data/Molecular data`.
</div>
</div>

![](figures/gui_menu.png)

<br />
<div class="panel panel-info">
<div class="panel-body">
Fill the search fields with the same information below and click on `Visualize Data`.
If you select `Filter  using clinical data` under the clinical filter we will also plot
the clinical information.
</div>
</div>

![](figures/gui_exp_query.png)

<br />
<div class="panel panel-info">
<div class="panel-body">
A plot with the summary of the data will be shown. 
</div>
</div>

![](figures/gui_exp_plots.png)
<br />
<div class="panel panel-info">
<div class="panel-body">

Also, if you want more details you 
can also open the `GDC search results: Results` section.
</div>
</div>

![](figures/gui_exp_query_results.png)

<br />
<div class="panel panel-info">
<div class="panel-body">

After the query is completed, you will be able to download the data and convert it to
an R object in the `Download & Prepare` section.
</div>
</div>

![](figures/gui_exp_prepare.png)
<br />
<div class="panel panel-info">
<div class="panel-body">
If successful it will give you a message where the data was saved.
</div>
</div>

![](figures/gui_exp_prepare_completed.png)
## Visualizing the Summarized Experiment

<br />
<div class="panel panel-info">
<div class="panel-body">
To visualize the SummarizedExperiment object select  `GDC Data/Manage SummarizedExperiment`:
</div>
</div>
![](figures/gui_visualize_se.png)

<br />
<div class="panel panel-info">
<div class="panel-body">

And click on `Select Summarized Experiment file`.
</div>
</div>
![](figures/gui_se_select.png)
<br />
<div class="panel panel-info">
<div class="panel-body">

Select the file downloaded from GDC.
</div>
</div>
![](figures/gui_se_selection.png)
<br />
<div class="panel panel-info">
<div class="panel-body">

You can access sample metadata
</div>
</div>
![](figures/gui_se_sampleinfo.png)

<br />
<div class="panel panel-info">
<div class="panel-body">
the assay data 
</div>
</div>
![Accessing  assay information from SummarizedExperiment](figures/gui_exp_se_assay.png)

<br />
<div class="panel panel-info">
<div class="panel-body">
or the features metadata
</div>
</div>
![Accessing features information from SummarizedExperiment ](figures/gui_exp_se_features.png)


## DNA methylation

<br />
<div class="panel panel-info">
<div class="panel-body">
Again, fill the search fields with the same information below and click on `Visualize Data`.
If you select `Filter using clinical data` under the clinical filter we will also plot
the clinical information.
</div>
</div>
![](figures/gui_dnamet_query.png)
<br />
<div class="panel panel-info">
<div class="panel-body">

A plot with the summary of the data will be shown.
</div>
</div>
![](figures/gui_dnamet_plots.png)

<br />
<div class="panel panel-info">
<div class="panel-body">
After the query is completed, you will be able to download the data and convert it to
an R object in the `Download & Prepare` section.
</div>
</div>
![](figures/gui_dnamet_prepare.png)

<br />
<div class="panel panel-info">
<div class="panel-body">
If successful it will give you a message where the data was saved.
</div>
</div>
![](figures/gui_dnamet_prepare_completed.png)

# Session Info

```{r sessioninfo, eval=TRUE}
sessionInfo()
```

# Bibliography
