Many disciplines, including Molecular Biology and Genetics, have become more and more data driven.

Starting now, we will use RStudio, a free software for data analysis

Most users of R are molecular biologists, but it is also used by economists, psychologists and marketing specialists

You will get a new window with an example text

It is a text file. One character takes one byte

Colors are only a guide for you. They are not part of the text

Today we will learn how to write text files for our course

This is not Microsoft Word

Today we will focus on a key idea.

To understand the data we need structure

For example, folders in the disk are a hierarchical structure.

Text documents also have a logical structure

• Letters form words
• Several words become phrases and paragraphs
• Paragraphs are contained in sections and chapters
• Sometimes we have lists of elements
• Sometimes we have tabular data
• Figures
• References to other works

Ordinary word processors are based on the WYSIWYG (What You See Is What You Get) philosophy

Users are encouraged to change fonts, sizes, colors and other visual attributes

Writing and formatting at the same time is distracting.

The idea is to write first, and format later, as close as possible to the time of publication.

• WYSIWYG: What You See Is What You Get
  • Microsoft Word
• Alternative: What You Mean Is What You Get
  • The information you enter defines the meaning of the document
  • The program generates beautiful output

• Sections
• Subsections
• paragraphs
• lists
  • numbered
  • unnumbered
• computer code

• figures
  • captions
• tables
  • headers
  • columns
• references
• metadata

• color
• font family
• font size
• centering
• number of sections

An alternative to ordinary Word Processors is to use text files with a few rules to mark the role of each element.

Text files can be read with any computer, and will be accessible for ever.

Today the Structured Text format most often used is Markdown

Here we show some of the rules

Consecutive lines of text are one paragraph. They are separated by an empty line

The first paragraph.

Another paragraph

The first paragraph.

Another paragraph

To show something remarkable, for example when someone important said something interesting.

> "The limits of my language mean
> the limits of my world"
> 
> *Ludwig Wittgenstein*

“The limits of my language mean the limits of my world”

Ludwig Wittgenstein

You have to indicate the web address of the image

![optional text](http://example.com/logo.png)

or the name of a file in the same directory

![optional text](images/logo.png)

Programs are usually written in a monospaced font.
That is, all letters have the same width.

```
this <- is.computer(code)
```

this <- is.computer(code)

This will be very important in the rest of the course

---
title: "Title"
author: "Author's name"
date: "4 October 2016"
output: html_document
---

Notice that the block is wrapped by --- (three hyphens)

We can speak about `x` and `data`

We can speak about x and data

• Help -> Markdown Quick Reference
• https://www.rstudio.org/links/r_markdown_cheat_sheet
• https://www.rstudio.org/links/r_markdown_reference_guide
• http://rmarkdown.rstudio.com/
• Google “Markdown”