This laboratory exercise is provided to introduce you to R and the RStudio environment. At the end of this exercise, you should be able to explain the concept of genome coverage, produce a quality plot of coverage along a chromosome and feel comfortable using and working in R and the RStudio environment. You will also learn the importance of reproducibility in bioinformatics research and make a script that they can use afterwards.
For this activity, we have provided a two page handout. Because R/RStudio changes, this is provided as a link to a google doc so that it may be updated. You can download it as a PDF so that you can print it to follow along.
You also have access to a one page handout that explains some of the concepts covered in the activity.
Finally, you will need to access the data: chr4.depth.out.
If you need practice loading data into R, this file (and all data files) can be found in the compressed directory all_data.tgz; click the link all_data.tgz and then select “Download” to save locally.
To quickly access chr4.depth.out add these data
to your workspace, by restoring our data object and assigning to your
data object (i.e.,
samtools.depth <- readRDS("data/activity1_data.rds").
To check your answers, we have also provided a key Activity 1 Key, for you after you are done with the assignment.