---
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
After launching the GUI select the `GDC Data/Get GDC data/Molecular data`.
![](figures/gui_menu.png)
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.
![](figures/gui_exp_query.png)
A plot with the summary of the data will be shown.
![](figures/gui_exp_plots.png)
Also, if you want more details you
can also open the `GDC search results: Results` section.
![](figures/gui_exp_query_results.png)
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.
![](figures/gui_exp_prepare.png)
If successful it will give you a message where the data was saved.
![](figures/gui_exp_prepare_completed.png)
## Visualizing the Summarized Experiment
To visualize the SummarizedExperiment object select `GDC Data/Manage SummarizedExperiment`:
![](figures/gui_visualize_se.png)
And click on `Select Summarized Experiment file`.
![](figures/gui_se_select.png)
Select the file downloaded from GDC.
![](figures/gui_se_selection.png)
You can access sample metadata
![](figures/gui_se_sampleinfo.png)
![Accessing assay information from SummarizedExperiment](figures/gui_exp_se_assay.png)
![Accessing features information from SummarizedExperiment ](figures/gui_exp_se_features.png)
## DNA methylation
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.
![](figures/gui_dnamet_query.png)
A plot with the summary of the data will be shown.
![](figures/gui_dnamet_plots.png)
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.
![](figures/gui_dnamet_prepare.png)
If successful it will give you a message where the data was saved.
![](figures/gui_dnamet_prepare_completed.png)
# Session Info
```{r sessioninfo, eval=TRUE}
sessionInfo()
```
# Bibliography