Difference between revisions of "CRG Introduction to R 2018"
From Bioinformatics Core Wiki
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This is an introductory course to R programming. | This is an introductory course to R programming. | ||
<br> The course is offered in 4 slow-paced practicums for <b>absolute beginners</b>. The goal is to offer a good base with a lot of hands on exercises.<br> | <br> The course is offered in 4 slow-paced practicums for <b>absolute beginners</b>. The goal is to offer a good base with a lot of hands on exercises.<br> | ||
| − | We will use [https://www.rstudio.com R Studio] | + | We will use the [https://www.rstudio.com R Studio] of the [http://rstudio01.linux.crg.es CRG server]. |
<br> | <br> | ||
| − | === Course | + | === Course Instructor === |
| − | * [mailto:sarah.bonnin@crg.eu Sarah Bonnin] | + | * [mailto:sarah.bonnin@crg.eu Sarah Bonnin] - Bioinformatician at the CRG bioinformatics core facility. |
<br> | <br> | ||
=== Dates, Time and Location === | === Dates, Time and Location === | ||
| − | * March 19-20 | + | * March 19-20 & April 16-17 |
* 10:00 - 14:00 | * 10:00 - 14:00 | ||
* PRBB Bioinformatics classroom (468). 4th floor. The hotel/North wing. | * PRBB Bioinformatics classroom (468). 4th floor. The hotel/North wing. | ||
| − | |||
<br> | <br> | ||
| Line 23: | Line 22: | ||
<br> | <br> | ||
* <b><u>Day 1</u></b> | * <b><u>Day 1</u></b> | ||
| − | ** Introduction to R Studio<br>We will use the R Studio [http://rstudio.linux.crg.es server] | + | ** Introduction to R Studio<br>We will use the [https://www.rstudio.com R Studio] of the [http://rstudio.linux.crg.es CRG server] (http://rstudio.linux.crg.es). We will go through what can be done with R Studio, from file and folder manipulation/navigation, to getting help on R functions. |
** Paths / directories | ** Paths / directories | ||
** Basics of R: syntax, create an object, manipulate the object, simple arithmetics. | ** Basics of R: syntax, create an object, manipulate the object, simple arithmetics. | ||
| Line 32: | Line 31: | ||
***Vectors<br>Basic (and most important) data structure in R. We will learn how to create, modify, subset, manipulate, compare vectors. | ***Vectors<br>Basic (and most important) data structure in R. We will learn how to create, modify, subset, manipulate, compare vectors. | ||
*** Introduction to factors: categorical vectors. | *** Introduction to factors: categorical vectors. | ||
| − | + | [[Media:1803_Introduction_to_R_day1.pdf|Slides day1]]<br> | |
| − | [[Media:|Slides day1]] | + | [[Media:1803_Exercises_day1.pdf|Exercises day 1 (1, 2 & 3)]]<br> |
| + | Correction of exercises: | ||
| + | * [[Media:Exercise1.R|Correction exercise 1]] | ||
| + | * [[Media:Exercise2.R|Correction exercise 2]] | ||
| + | * [[Media:Exercise3.R|Correction exercise 3]] | ||
<br> | <br> | ||
| − | [[Media:|Exercises day1]] | + | <!-- [[Media:|Exercises day1]]--> |
<br> | <br> | ||
* <b><u>Day 2</u></b> | * <b><u>Day 2</u></b> | ||
** Missing values: how to deal with NA values. | ** Missing values: how to deal with NA values. | ||
| − | ** Matrices & data frames<br>2-dimensional objects: how to create, subset, manipulate. | + | ** Matrices & data frames<br>2-dimensional objects: how to create, subset, select, manipulate. |
| − | [[Media:|Slides day2]] | + | [[Media:1803_Introduction_to_R_day2.pdf|Slides day2]]<br> |
| − | <br> | + | [[Media:1803_Exercises_day2.pdf|Exercises day 2 (4 & 5)]]<br> |
| − | [[Media:|Exercises | + | Correction of exercises: |
| + | * [[Media:Exercise4.R|Correction exercise 4]] | ||
| + | * [[Media:Exercise5.R|Correction exercise 5]] | ||
<br> | <br> | ||
* <b><u>Day 3</u></b> | * <b><u>Day 3</u></b> | ||
| + | ** Input / output<br>Reading in and writing out files. Adapting I/O to file format. | ||
** Library / packages<br>Install and load packages. Look for functions in those packages. | ** Library / packages<br>Install and load packages. Look for functions in those packages. | ||
| − | + | [[Media:1804_Introduction_to_R_day3.pdf|Slides day3]]<br> | |
| − | [[Media:| | + | [[Media:1804_Exercises_day3.pdf|Exercises day 3 (6 & 7)]]<br> |
| − | <br> | + | Correction of exercises: |
| − | [[Media:| | + | * [[Media:Exercise6.R|Correction exercise 6]] |
| + | * [[Media:Exercise7.R|Correction exercise 7]] | ||
<br> | <br> | ||
* <b><u>Day 4</u></b> | * <b><u>Day 4</u></b> | ||
| Line 55: | Line 62: | ||
** Introduction to ggplot2 package<br>ggplot2 provides functions for creating and customizing plots. We will learn the basic structure and how to produce simple plots. | ** Introduction to ggplot2 package<br>ggplot2 provides functions for creating and customizing plots. We will learn the basic structure and how to produce simple plots. | ||
** Input / output<br>We will save plots as files in different formats, both from R Studio and from the terminal. | ** Input / output<br>We will save plots as files in different formats, both from R Studio and from the terminal. | ||
| − | [[Media:|Slides day4]] | + | [[Media:1804_Introduction_to_R_day4.pdf|Slides day4]]<br> |
| − | <br> | + | [[Media:1804_Exercises_day4.pdf|Exercises day 4 (8 & 9)]]<br> |
| − | [[Media:|Exercises | + | Correction of exercises: |
| + | * [[Media:Exercise8.R|Correction exercise 8]] | ||
| + | * [[Media:Exercise9.R|Correction exercise 9]] | ||
| − | + | === Resources === | |
| + | *[https://www.rstudio.com/resources/cheatsheets/ R Studio cheat sheets] | ||
| + | * [https://www.r-bloggers.com/ R bloggers] | ||
| + | * [https://www.r-graph-gallery.com/ R graph gallery] | ||
| + | *[https://www.statmethods.net/index.html Quick R] | ||
| + | *[http://www.cookbook-r.com/ Cookbook for R] | ||
| + | *[https://cran.r-project.org/doc/contrib/Paradis-rdebuts_en.pdf R for beginners - CRAN website] | ||
| + | *[http://style.tidyverse.org/ R Style guide] | ||
| + | *[https://www.datacamp.com/courses/free-introduction-to-r DataCamp: interactive introduction to R] | ||
Latest revision as of 15:38, 17 April 2018
Contents
Description
This is an introductory course to R programming.
The course is offered in 4 slow-paced practicums for absolute beginners. The goal is to offer a good base with a lot of hands on exercises.
We will use the R Studio of the CRG server.
Course Instructor
- Sarah Bonnin - Bioinformatician at the CRG bioinformatics core facility.
Dates, Time and Location
- March 19-20 & April 16-17
- 10:00 - 14:00
- PRBB Bioinformatics classroom (468). 4th floor. The hotel/North wing.
Course Syllabus, Schedule, and Materials
The day before each session, the slides will be uploaded in case you want to print them.
- Day 1
- Introduction to R Studio
We will use the R Studio of the CRG server (http://rstudio.linux.crg.es). We will go through what can be done with R Studio, from file and folder manipulation/navigation, to getting help on R functions. - Paths / directories
- Basics of R: syntax, create an object, manipulate the object, simple arithmetics.
- Functions usage in R
Arguments. Get help. - R scripts: write and save commands, run them as a block. Comment code.
- Data types.
- Data structures:
- Vectors
Basic (and most important) data structure in R. We will learn how to create, modify, subset, manipulate, compare vectors. - Introduction to factors: categorical vectors.
- Vectors
- Introduction to R Studio
Slides day1
Exercises day 1 (1, 2 & 3)
Correction of exercises:
- Day 2
- Missing values: how to deal with NA values.
- Matrices & data frames
2-dimensional objects: how to create, subset, select, manipulate.
Slides day2
Exercises day 2 (4 & 5)
Correction of exercises:
- Day 3
- Input / output
Reading in and writing out files. Adapting I/O to file format. - Library / packages
Install and load packages. Look for functions in those packages.
- Input / output
Slides day3
Exercises day 3 (6 & 7)
Correction of exercises:
- Day 4
- Basic plotting (base graphics package)
Scatter plots, boxplots, barplots, pie plots, histograms. - Introduction to ggplot2 package
ggplot2 provides functions for creating and customizing plots. We will learn the basic structure and how to produce simple plots. - Input / output
We will save plots as files in different formats, both from R Studio and from the terminal.
- Basic plotting (base graphics package)
Slides day4
Exercises day 4 (8 & 9)
Correction of exercises:
