Practical applications of learned concepts in R

Example

TBD

Please run the code provided to replicate some of the analyses. Make sure you can explain what all the analysis steps do and that you understand all the results.

In addition, there are some extra tasks (Task 1), where no R code is provided. Please do these tasks when you have time available at the end of the lab.

Load the data

Read the data, and convert to matrix format.

mrna <- read.table("data/data_example.txt", header=T, sep="\t", dec=".")

# Convert to matrix format

mrna <- as.matrix(mrna)

Print the data

mrna[1:4, 1:4]
      OSL2R.3002T4 OSL2R.3005T1 OSL2R.3013T1 OSL2R.3030T2
ACACA      1.60034     -0.49087     -0.26553     -0.27857
ANXA1     -2.42501     -0.05416     -0.46478     -2.18393
AR         0.39615     -0.43348     -0.10232      0.58299
BAK1       0.78627      0.39897      0.22598     -1.31202

Visualize the overall distribution of expression levels by histogram

hist(mrna, nclass=40, xlim=c(-5,5), col="lightblue")

Task 1

This is a callout-note, and it can be quite useful for exercises. You can find more about callout here.

Example: Extend the above analysis to cover all genes.