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improve polls and update for Nov 2024
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Natalie Elphick
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5 changed files with 171 additions and 187 deletions
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title: "Introduction to R Data Analysis"
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subtitle: "Part 1"
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author: "Natalie Elphick"
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date: "August 26th, 2024"
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date: "November 11th, 2024"
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knit: (function(input, ...) {
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rmarkdown::render(
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input,
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@ -29,8 +29,7 @@ knitr::opts_chunk$set(comment = "")
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**Natalie Elphick**
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Bioinformatician I
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**Min-Gyoung Shin**
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Bioinformatician III
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## Poll 1
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@ -246,19 +245,27 @@ DogBreeds <- c("Labrador Retriever", "Akita", "Bulldog")
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- Decimal numbers
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- Logical
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- Boolean (TRUE, FALSE)
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- NA (missing data)
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- Character
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- Letters and strings of letters
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- "A", "Labrador Retriever"
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## Missing Values
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- R has a special data type - NA which represents missing data
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- NAs can take the place of any type but by default are logical
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```{r}
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NA + 1
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```
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## Poll 3
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**Which of these is not the correct data type for the value?**
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1. 1.5 - Numeric
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2. "1" - Character
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3. NA - Logical
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4. 1 - Integer
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1. "1.5" - Numeric
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2. "A" - Character
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3. 1L - Integer
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4. TRUE - Boolean
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## Data Structures
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@ -320,17 +327,7 @@ x >= y # Greater than or equal to
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x %in% y # Is x in this vector y?
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```
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## Poll 4
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**What is the output of the following code?**
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```{r, eval = FALSE}
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4 %in% c(1, 2, 3, 4)
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```
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1. TRUE
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2. FALSE
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3. NA
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## Logical Operators
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@ -344,6 +341,18 @@ x | y # x or y
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x & y # x and y
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```
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## Poll 4
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**What is the output of the following code?**
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```{r, eval = FALSE}
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2 + 2 == 4 & 8 + 10 < 20
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```
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1. TRUE
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2. FALSE
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3. NA
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## Poll 5
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**What is the output of the following code?**
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@ -351,7 +360,7 @@ x & y # x and y
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x <- TRUE
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y <- FALSE
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x & !y
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y | (y | x)
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```
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1. TRUE
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@ -470,16 +479,17 @@ packages
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## Upcoming Workshops
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[Intermediate RNA-Seq Analysis Using R](https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-5)
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September 10, 2024 9am-12pm PDT
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[Introduction to scATAC-seq Data Analysis](https://gladstone.org/events/introduction-scatac-seq-data-analysis)
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November 14 - November 15, 2024 1:00-4:00pm PST
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[Introduction to Statistics, Experimental Design, and Hypothesis Testing](https://gladstone.org/events/introduction-statistics-experimental-design-and-hypothesis-testing-1)
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September 10 - September 12, 2024 1-3pm PDT
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[Introduction to Linear Mixed Effects Models](https://gladstone.org/events/introduction-linear-mixed-effects-models-0)
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November 18-November 19, 2024 1:00-3:00pm PST
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[Single Cell RNA-Seq Data Analysis](https://gladstone.org/events/single-cell-rna-seq-data-analysis-0)
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September 16-September 17, 2024 9am-4pm PDT
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[scATAC-seq and scRNA-seq Data Integration](https://gladstone.org/events/scatac-seq-and-scrna-seq-data-integration)
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November 22, 2024 1:00-4:00pm PST
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- Check [this link](https://gladstone.org/events?series=data-science-training-program) at for the full schedule
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@ -31,11 +31,8 @@ knitr::opts_chunk$set(comment = "")
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**Natalie Elphick**
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Bioinformatician I
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**Michela Traglia**
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Senior Statistician
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**Ayushi Agrawal**
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Bioinformatician III
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**Reuben Thomas**
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Associate Core Director
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# Schedule
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@ -281,30 +278,23 @@ For any bioinformatics specific questions feel free to reach out to the Gladston
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# Additional Resources
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## Coding Templates
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## R
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Code templates can be used to avoid typing the same code over and over again.
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- These are templates that we are using to automate things like plot appearance and documentation:
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- [.Rmd Template](https://www.dropbox.com/scl/fi/a9cnyqdajgabbfcxbmm6y/RMD_template.Rmd?rlkey=yntfpo6aptw9b4pgjyzpe5ubi&dl=1)
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- [.R Script Template](https://www.dropbox.com/scl/fi/cy43b8b1x3nzn17esnmmt/Rscript_template.R?rlkey=zn7b0g8nn0s9213blh70fjjsx&dl=1)
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## R Resources
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- [R for Data Science](https://r4ds.hadley.nz/)
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- [Top 10 R Errors and How to Fix them](https://statsandr.com/blog/top-10-errors-in-r/)
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- [R Markdown: The Definitive Guide](https://bookdown.org/yihui/rmarkdown/how-to-read-this-book.html)
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- [ggplot2: elegant graphics for data analysis](https://ggplot2-book.org/)
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- [Advanced R](https://adv-r.hadley.nz/)
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## Statistics
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- [Data Analysis in R](https://bookdown.org/steve_midway/DAR) : This book has more statistics details than *R for Data Science*
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- [Generalized Linear Models](https://bookdown.org/steve_midway/DAR/glms-generalized-linear-models.html)\
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- [Random Effects](https://bookdown.org/steve_midway/DAR/random-effects.html)
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## RNA-seq Analysis
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- [RNA-seqlopedia](https://rnaseq.uoregon.edu/) : Everything you need to know about RNA-seq experiments
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- [RNA-seq Expression Units](https://luisvalesilva.com/datasimple/rna-seq_units.html) : Blog post on understanding common units
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- [Introduction to Single-Cell Analysis with Bioconductor](https://bioconductor.org/books/3.17/OSCA.intro/index.html) : Covers the basics of scRNA-seq analysis in R
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## Dimensional Reduction
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- [Tutorial on PCA](https://uw.pressbooks.pub/appliedmultivariatestatistics/chapter/pca/) : PCA explained with R code examples
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- [Understanding UMAP](https://pair-code.github.io/understanding-umap/) : Short explanation with great visualizations, mainly useful for scRNA-seq analysis
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## Upcoming Workshops
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[Intermediate RNA-Seq Analysis Using R](https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-5)
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September 10, 2024 9am-12pm PDT
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[Introduction to scATAC-seq Data Analysis](https://gladstone.org/events/introduction-scatac-seq-data-analysis)
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November 14 - November 15, 2024 1:00-4:00pm PST
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[Introduction to Statistics, Experimental Design, and Hypothesis Testing](https://gladstone.org/events/introduction-statistics-experimental-design-and-hypothesis-testing-1)
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September 10 - September 12, 2024 1-3pm PDT
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[Introduction to Linear Mixed Effects Models](https://gladstone.org/events/introduction-linear-mixed-effects-models-0)
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November 18-November 19, 2024 1:00-3:00pm PST
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[Single Cell RNA-Seq Data Analysis](https://gladstone.org/events/single-cell-rna-seq-data-analysis-0)
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September 16-September 17, 2024 9am-4pm PDT
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[scATAC-seq and scRNA-seq Data Integration](https://gladstone.org/events/scatac-seq-and-scrna-seq-data-integration)
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November 22, 2024 1:00-4:00pm PST
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- Check [this link](https://gladstone.org/events?series=data-science-training-program) at for the full schedule
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This guide will help you get set up for <ins>Intro to R Data Analysis</ins>. There are just a few steps to make sure you'll have the necessary software installed and ready to go on day 1. **Please ensure that you've completed each step by running the validation test prior to the start of the workshop**.
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This guide will walk you through how to install R, RStudio, and some additional tools that we’ll be using in the course. By rough analogy to a car, R is like the car’s engine and RStudio is like the dashboard. More precisely, R is a programming language and Rstudio is an ‘integrated development environment’ (IDE), which is basically a nice software interface for interacting with R. For our purposes, you will only ever interact directly with RStudio, but it needs to have R installed to work (like a car needing its engine).
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This guide will help you set up R, RStudio, and a few extra tools we'll use in this course. You can think of R as the engine that powers everything, while RStudio is like the dashboard that makes it easy to control. R is a programming language, and RStudio is a tool that helps you work with it. Even though you'll mainly use RStudio, it needs R to be installed to work, just like a car needs an engine to run.
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Please complete the following steps (must be done in this order). If you already have R and Rstudio installed you can skip ahead. Make sure you complete step 5 though!
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@ -83,4 +83,4 @@ You should see a plot that looks like this appear:
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</center>
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If you see an error that says “R version is too old” that means you need to update your R version. The update process is the same as the installation process. It will update your R installation. If you see an error that says “There is no package called ggplot2” that means you need to install the tidyverse package (see above).
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If you see an error that says “R version is too old” that means you need to update your R version. The update process is the same as the installation process. It will update your R installation. If you see an error that says “There is no package called ggplot2” that means you need to install the tidyverse package (see the *Install Required Packages* section).
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