Introduction to R

At this point we have learned:

• How to work at the Linux command line
• How to document our work with Markdown
• How to save and track our work, and collaborate with Git
• How to run BLAST at the command line
• How to automate repetitive tasks with for loops

GOOD JOB!

We have identified a candidate virus genome associated with respiratory illness in our patient.

Next, we would like to:

• Summarize and explore differences in the BLAST results in more detail
• Build a phylogenetic tree to better understand the origin of the candidate virus
  • We have ~ 2500 hits to the candidate virus
  • Need to reduce these to a smaller number

To accomplish these goals we will start learning R

• BLAST results on hold
• Learn some R
  • R markdown
  • Setting up git in RStudio
  • Tutorials: swirl
  • Tutorials: tidyverse
• Practice, resume BLAST analysis

summary(cars)

     speed           dist       
 Min.   : 4.0   Min.   :  2.00  
 1st Qu.:12.0   1st Qu.: 26.00  
 Median :15.0   Median : 36.00  
 Mean   :15.4   Mean   : 42.98  
 3rd Qu.:19.0   3rd Qu.: 56.00  
 Max.   :25.0   Max.   :120.00