Skip to content

Storage room

Séance 5 : Advanced manipulation of Data Objects

Séance 5 : Structures de contrôle

Séance 6 et 7 : Les fonctions

Séance 8 et 9 : Les graphiques en R

Séance 10 : Récapitulatif général du savoir faire pour application à l'analyse SingleCell RNA-Seq

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
    Data structure - Factor : [https://r4ds.hadley.nz/factors.html](https://r4ds.hadley.nz/factors.html) : R for Data Science (O'Reilly Book tidyverse) 2e : Chapter 17



* Tutorials : 
    * O’Reilley Book 1 Hands-On Programming with R
        * [2 The Very Basics | Hands-On Programming with R](https://rstudio-education.github.io/hopr/basics.html#objects)
        * [https://rstudio-education.github.io/hopr/r-objects.html#atomic-vectors](https://rstudio-education.github.io/hopr/r-objects.html#atomic-vectors)
    * Introduction à R (Français)
        * [https://egallic.fr/Enseignement/R/Book/introduction.html](https://egallic.fr/Enseignement/R/Book/introduction.html) (Chapter 1)
        * 
    * Brendan R. E. Ansell : Introduction to R - tidyverse
        * [https://bookdown.org/ansellbr/WEHI_tidyR_course_book/welcome-to-r.html#variables](https://bookdown.org/ansellbr/WEHI_tidyR_course_book/welcome-to-r.html#variables)
        * [https://bookdown.org/ansellbr/WEHI_tidyR_course_book/welcome-to-r.html#vectors](https://bookdown.org/ansellbr/WEHI_tidyR_course_book/welcome-to-r.html#vectors)
    * Guide R Joseph Larmarange (Français)
        * [https://larmarange.github.io/guide-R/bases/vecteurs.html](https://larmarange.github.io/guide-R/bases/vecteurs.html) + utile pour les fonctions de bases aussi
        *

Session 3

Best practices :

Séances 2 et 3 : Les objets R

Data structure - Data-frames : https://bookdown.org/ansellbr/WEHI_tidyR_course_book/welcome-to-r.html#data-frames : Brendan R. E. Ansell : Introduction to R - tidyverse - Chapter 1.14

https://rstudio-education.github.io/hopr/r-notation.html#dollar-signs-and-double-brackets

idées questions

  1. Which variable names are incorrect :

Packages

[https://hbctraining.github.io/Intro-to-R-flipped/lessons/04_introR_packages.html]

R works in a model of package “add-ons” where packages are collections of functions, data sets, and other resources that extend the functionality of the base R system.

As R is used by many communities (biologists, economists, statisticians, meteorologists…), several R packages were designed to address specific tasks or provide specialized tools for the different domains or areas of interest.

Therefore, many (most) of R packages are available in the official CRAN package repository but we will also use packages from Bioconductor (open source software for Bioinformatics).

When you start an R session, default packages are automatically loaded allowing you to use R as a calculator and access basic mathematical functions. Some of the key default packages include:

  • base: It provides basic data structures (vectors, matrices, data frames, lists), operators for calculations (+, -, *, /), control structures (if-else, loops), and functions for mathematical operations, such as log(), sin(), cos(), and many more.
  • stats: This package contains functions for statistical analysis and modeling. It includes methods for probability distributions, hypothesis testing, regression, analysis of variance, and other statistical procedures. Some commonly used functions from this package are mean(), sd() or t.test().
  • graphics: The graphics package provides functions for creating plots and visualizations. It includes functions for basic plots (scatter plots, bar plots, histograms), customization options, and annotation features. The functions plot(), hist() or boxplot() are examples of functions available in this package.
  • utils: This package contains utility functions that assist in data manipulation, file handling, and other miscellaneous tasks. Functions like head(), tail(), str(), and install.packages() are part of this package._ _

To be able to use the functionalities of a R package, you need to load the package in your current R environment. Here is a small video to show you how to install, load R packages.

How to install an R package