--- 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)
the assay data
![Accessing assay information from SummarizedExperiment](figures/gui_exp_se_assay.png)
or the features metadata
![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