Terminating Your Instance

  1. Go to your AWS E2C machines
  2. Select machines to terminate (Note you have machines running in two or three locations: Virgina and Oregon OR Califonia)
  3. Select Actions > Change Termination Protection
  4. Select Yes Disable
  5. Select Actions > Instance State > Terminate
  6. After both instances are terminated select Elastic IPs
  7. Select Actions > Release addresses
  8. Then go back to N. California or Oregon
  9. Select Volumes on the left hand side
  10. Right click your Volume and select Delete Volume

Fix names for GWAS

It turns out that wgs in SNPassoc does not know how to deal with names that have spaces in them.

i.e. if you want to do a a GWAS on Amylose content it won’t work unless you change the name.

Change the name like this to get rid of the space:

colnames(snps3)[colnames(snps3)=="Amylose content"] <- "Amylose.content"

How to turn in your Rmd assignments

One of the advantages of working in R markdown is that the code and its output can all be included in the same document.

There are two different ways to do this; both will work.

Here are detailed instructions.

  1. Include your code in the R markdown file. Any answer that requires any computation should include the code used to answer the question. For example, for question 8 “How many hits have an e-value of 0?” or “Recalculate the above values but in percentage of hits rather than absolute values.” Do not just type in a number. Instead include the code in your Rmd that will generate the answer.
  2. Click the “Preview” Button generate an up-to-date html version of your notebook. Check it to make sure you are happy with its content. Make sure it includes your code and output
  3. An alternative is to click the triangle next the the preview button and then choose “knit-to-html”. This will re-run all code in your document and generate a new html document; it ensures that your the R output matches the code in your document and so is “best practice”. Note that if you choose this option, when you “knit” your file R will run all of the code in the .Rmd in a new environment. This means that if your code depends on objects created by code in the lab manual, then that code also most be included so that you knit your file successfully.
  4. Add BOTH your .Rmd AND the .html file(s) to your repository. If you used “knit” you will actually have two .html files, one that ends .nb.html and just one that ends in .html. The knitted file is the one without .nb, but if you are unsure just add them both.
  5. Commit your changes
  6. Push

Welcome to BIS180L

Welcome to the BIS180L website for 2018.

We will be updating material over the next couple of weeks in anticipation of this Spring’s offering.


Professor Maloof

Reading Material / Text Book

We will use Vince Buffalo’s excellent book Bioinformatics Data Skills.

This book is available online for free through the UC Davis Library (on campus or VPN connection required). UC is licensed for simultaneous access by 28 people. If that doesn’t work for you, you can buy it direct from the publisher or from amazon. As of this posting Amazon is cheaper and has used copies as well.

Additionally we will use Hadley Wickham’s also excellent book R for Data Science which is available online for free. If you would like a physical copy, here is the amazon link