---
title: "Access GSE159526 data using Bioconductor's ExperimentHub"
author: 
  - name: Victor Yuan
    affiliation:
    - University of British Columbia, Vancouver, Canada
    email: vyuan@bcchr.ca
output: 
  BiocStyle::html_document:
    self_contained: yes
    toc: true
    toc_float: true
    toc_depth: 2
    code_folding: show
date: "`r doc_date()`"
package: "`r pkg_ver('GSE159526')`"
vignette: >
  %\VignetteIndexEntry{Introduction to GSE159526}
  %\VignetteEncoding{UTF-8}  
  %\VignetteEngine{knitr::rmarkdown}
editor_options: 
  chunk_output_type: console
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    
    crop = NULL 
    #https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016656.html
)
```


```{r vignetteSetup, echo=FALSE, message=FALSE, warning = FALSE}
## Track time spent on making the vignette
startTime <- Sys.time()

## Bib setup
library("RefManageR")

## Write bibliography information
bib <- c(
    R = citation(),
    BiocStyle = citation("BiocStyle")[1],
    knitr = citation("knitr")[1],
    RefManageR = citation("RefManageR")[1],
    rmarkdown = citation("rmarkdown")[1],
    sessioninfo = citation("sessioninfo")[1],
    testthat = citation("testthat")[1],
    GSE159526 = citation("GSE159526")[1]
)
```

# How to access GSE159526 with Bioconductor

## Citing `GSE159526`

We hope that `r Biocpkg("GSE159526")` will be useful for your research. Please 
use the following information to cite the package and the overall approach. 
Thank you!

```{r "citation"}
## Citation info
citation("GSE159526")
```

# Quick start to using to `GSE159526`

There are 3 objects associated with GSE159526:

**EH6130** - Raw DNA methylation data, .idat files read into r with `minfi` and 
saved as an `rgset` object.

**EH6131** - Processed filtered DNA methylation data. Described in 
`r Citep(bib[["GSE159526"]])`.

**EH6132** - Sample information stored as a `tibble`/`data.frame` object.

```{r "start", message=FALSE, eval=FALSE}
eh <- ExperimentHub()
query(eh, "GSE159526")

# raw rgset
library(minfi)
GSE159526_rgset <- eh[['EH6130']] # requires minfi

# normalized processed data matrix
GSE159526_data <- eh[['EH6131']]

# sample information
GSE159526_pdat <- eh[['EH6132']]
```

# Reproducibility

The `r Biocpkg("GSE159526")` package `r Citep(bib[["GSE159526"]])` was made 
possible thanks to:

* R `r Citep(bib[["R"]])`
* `r Biocpkg("BiocStyle")` `r Citep(bib[["BiocStyle"]])`
* `r CRANpkg("knitr")` `r Citep(bib[["knitr"]])`
* `r CRANpkg("RefManageR")` `r Citep(bib[["RefManageR"]])`
* `r CRANpkg("rmarkdown")` `r Citep(bib[["rmarkdown"]])`
* `r CRANpkg("sessioninfo")` `r Citep(bib[["sessioninfo"]])`
* `r CRANpkg("testthat")` `r Citep(bib[["testthat"]])`

This package was developed using `r BiocStyle::Biocpkg("biocthis")`.

Code for creating the vignette:

```{r createVignette, eval=FALSE}
## Create the vignette
library("rmarkdown")
system.time(render(here::here("vignettes", "GSE159526.Rmd"), 
                   "BiocStyle::html_document"))

## Extract the R code
library("knitr")
knit("GSE159526.Rmd", tangle = TRUE)
```

Date the vignette was generated.

```{r reproduce1, echo=FALSE}
## Date the vignette was generated
Sys.time()
```

Wallclock time spent generating the vignette.

```{r reproduce2, echo=FALSE}
## Processing time in seconds
totalTime <- diff(c(startTime, Sys.time()))
round(totalTime, digits = 3)
```

`R` session information.

```{r reproduce3, echo=FALSE}
## Session info
library("sessioninfo")
options(width = 120)
session_info()
```

# Bibliography

This vignette was generated using `r Biocpkg("BiocStyle")` 
`r Citep(bib[["BiocStyle"]])` with `r CRANpkg("knitr")` 
`r Citep(bib[["knitr"]])` and `r CRANpkg("rmarkdown")` 
`r Citep(bib[["rmarkdown"]])` running behind the scenes.

Citations made with `r CRANpkg("RefManageR")` `r Citep(bib[["RefManageR"]])`.

```{r vignetteBiblio, results="asis", echo=FALSE, warning=FALSE, message=FALSE}
## Print bibliography
PrintBibliography(bib, .opts = list(hyperlink = "to.doc", style = "html"))
```