DFCI Introduction to R and RStudio

Transcript

1. Introduction to R/RStudio Patrick Kimes, PhD Postdoctoral Fellow Dana-Farber Cancer Institute Harvard TH Chan School of Public Health Top Ten Seminars October 1, 2019
2. October 1, 2019 October 22, 2019 November 12, 2019 December 10, 2019 January 21, 2020 February 11, 2020 March 17, 2020 April 14, 2020 May 19, 2020 June 16, 2020 Introduction to R and RStudio Data visualization with ggplot2 Data visualization principles and plots to avoid Design of Clinical Trials Basics Correlation: you are probably using it wrong How to detect and deal with batch effects Brief introduction to machine learning Culprits of the reproducibility crisis: multiple testing and p-hacking Experimental Design: How many size and should I pool? Detecting differentially expressed genes with RNA-seq top ten seminars in data science
3. R and RStudio?
4. R and RStudio? programming language R think Java, C, C++, Python, …
5. RStudio programming language R and RStudio? software to make data analysis with R easier
6. RStudio programming language R and RStudio? programming language R software to make data analysis with R easier
8. RStudio engine R dashboard
9. why R and RStudio?
10. what about SAS? why R and RStudio?
11. what about SAS? • R is free, open source • R is the home of new methods • R has a large, active community • R is highly interoperable, extensible why R and RStudio?
12. what about Python? why R and RStudio?
13. what about Python? • Good question! Up to you! • R is arguably easier to learn • R has more statistical tools • R makes exploration and visualization easier why R and RStudio?
14. why R and RStudio?
15. it gets you to the data fast! why R and RStudio?
16. it gets you to the data fast! and that’s fun! https://twitter.com/avogado6/status/1165595520967954432
17. who already has R / RStudio installed?
18. how to install R and RStudio
20. how to install R and RStudio 1. Search “R”, 
 Search “RStudio” 2. Install “R”, 
 Install “RStudio”
21. how to install R and RStudio 1. Search “R”, 
 Search “RStudio” 2. Install “R”, 
 Install “RStudio” maybe a few more steps so please do this later a much better guide: rafalab.github.io/dsbook/installing-r-rstudio
22. lucky us! we have a workaround! https://rstudio.cloud
23. lucky us! we have a workaround! https://rstudio.cloud do this
24. lucky us! we have a workaround! https://rstudio.cloud this too
25. lucky us! we have a workaround! https://rstudio.cloud select [from Git repo]
26. lucky us! we have a workaround! https://rstudio.cloud enter https://github.com/pkimes/dfci-introR
27. welcome to RStudio!
28. local RStudio select [New Project]
29. local RStudio select [Version Control]
30. local RStudio we’ll use [Git]
31. local RStudio enter https://github.com/pkimes/dfci-introR
32. we’re good to go!
33. you now have a project! what’s an RStudio project? basically a folder to organize an analysis • input data • R scripts • results/figures
34. coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding let’s give it a try!
35. arithmetic variables functions help installing packages loading packages for-loops what did we (hopefully) cover?
36. some pieces in the modern (R) data scientist’s toolbox
37. some pieces in the modern (R) data scientist’s toolbox rmarkdown tidyverse shiny [bioconductor] documentation, communication data manipulation, visualization web application framework community of genomics packages
38. some pieces in the modern (R) data scientist’s toolbox rmarkdown tidyverse shiny [bioconductor] documentation, communication data manipulation, visualization web application framework community of genomics packages
39. .R file
40. .R file .Rmd file
41. .R file .Rmd file formal header
42. .R file .Rmd file code “chunks”
43. .R file .Rmd file plain text (markdown)
44. .R file .Rmd file specified output format
45. .Rmd file
46. .Rmd file formatted text output! R code
47. rmarkdown documentation, communication myfile.Rmd markdown + R code chunks
48. rmarkdown documentation, communication myfile.Rmd markdown + R code chunks markdown myfile.md execute R code
49. rmarkdown documentation, communication myfile.Rmd markdown + R code chunks markdown myfile.md execute R code pandoc conversion
50. rmarkdown documentation, communication rmarkdown.rstudio.com
51. coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding let’s give it a try!
52. what did we (hopefully) cover? create a new Rmd file writing simple markdown creating code chunks executing code knitting documents
53. some pieces in the modern (R) data scientist’s toolbox rmarkdown tidyverse shiny [bioconductor] documentation, communication data manipulation, visualization web application framework community of genomics packages
54. some pieces in the modern (R) data scientist’s toolbox rmarkdown tidyverse shiny [bioconductor] documentation, communication data manipulation, visualization web application framework community of genomics packages
55. tidyverse data manipulation, visualization tidyverse.org
56. some pieces in the modern (R) data scientist’s toolbox rmarkdown tidyverse shiny [bioconductor] documentation, communication data manipulation, visualization web application framework community of genomics packages
57. shiny web application framework shiny.rstudio.com
58. shiny web application framework shiny.rstudio.com/gallery/kmeans-example
59. some pieces in the modern (R) data scientist’s toolbox rmarkdown tidyverse shiny [bioconductor] documentation, communication data manipulation, visualization web application framework community of genomics packages
60. bioconductor community of genomics packages bioconductor.org
61. bioconductor community of genomics packages CRAN Bioconductor • genomic focus • software • annotations • data • package reviews • scope • consistency
62. awesome!
63. where do we go from here?
64. where do we go from here? wait, I’m lost
65. introduction to data science rafalab.github.io/dsbook
66. RStudio Cloud tutorials rstudio.cloud
67. r4ds.had.co.nz R for data science
68. learn the tidyverse tidyverse.org/learn
69. advanced R adv-r.hadley.nz
70. biomedical data science open online training rafalab.github.io/pages/harvardx
71. … and because it’s 2019, deep learning tensorflow.rstudio.com
72. questions? wait, I’m still lost