R tutorial

TODO

Tasks available from web which utilze example data available in R - object assignment, subsetting, plotting, mathematical functions, sorting etc (20 tasks?)

• Usage/interaction within environment
• Bioconductor resources/vignettes(including downloading)
• Bioconductor basics (any resources for limma out there?)

Twenty tasks to do in R

• Use a contributed guide as a template fo a list of twenty tasks to do. It must cover;

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Resources

• Quickest way to learn R: use the Contributed Documentation (http://cran.stat.auckland.ac.nz/other-docs.html)
• Thousands of pages of documentation including short guides / reference cards

Command prompt

• Type commands after the prompt (>) e.g.

> x <- 1:10        # assignment of 1 to 10 to an object called 'x'
> x                # Returning the x object to the screen
 [1]  1  2  3  4  5  6  7  8  9 10

• Continuation of commands is expected after the plus symbol (+) e.g.

> x <- 1:          # partial command: parser is expecting more information
+  10
> x
 [1]  1  2  3  4  5  6  7  8  9 10

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Obtaining help in R

help.start()           # Browser based help documentation
help()                 # Help on a topic
? ls                   # alternative help method on ls function
apropos(mean)          # Find Objects by (Partial) Name
example(mean)          # Run an Examples Section from the Online Help
demo()                 # Demonstrations of R Functionality
demo(graphics)         # Demonstration or graphics Functionality
data()                 # Publically available datasets

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Useful commands in the R environment

search()              # Give Search Path for R Objects
searchpaths()         # Give Full Search Path for R Objects
ls()                  # List objects
objects()             # alternate function to list objects
rm(list=ls())         # Remove Objects from a Specified Environment
save.image()          # Save R Objects
q()                   # Terminate an R Session →  prompted to Save workspace image? [y/n/c]:

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• • Memory based, can write to → .RData file

• File handling
• Object creation
• Different types of data
• Quiting R
• Recommended contributed guide/reference card

Contributed material

• usingR-2.pdf Chapter 1 → Starting up.
• MGEDI → installing R/Bioconductor p30 - p34 (documentation/help)

1. Create a vector
2. Create a matrix
3. Create a list
4. Subsetting/Indexing
5. Indexing from a vector
6. Indexing from a matrix
7. Indexing from a list
8. Plotting data
9. Labelling/colours etc
10. Ab lines?
11. how to read help
12. Apropos/example/demo/find etc
13. Help example
14. ls/rm
15. quit