Week 4 - Homework

week04
homework

Write your code directly in a Quarto document.

To create a Quarto document: go to File -> New File -> Quarto Document, then click Create.

  1. Import the read-counts.csv file.

Quick reminder: this data file contains gene expression values of samples from four groups, sample names are prefixed by “WT.”, “SET1.”, “SET1.RRP6.” and “RRP6.”. Each group has 10 samples.

  1. Create a function to calculate the average gene expression across samples by selected group. Test your function on WT samples.
  1. Use function created in question 2 to calculate the average for all sample groups, store the results in a list. Show the first 5 average gene expression of SET1.RRP6 samples.
  1. Transform the list obtained in question 3 to a data frame using as.data.frame(). Show the head lines of your data frame.
Tip

A data frame can be considered as a list of equal-length vectors.

  1. What are the genes having an average greater than 10000 in WT and SET1 samples? Compare if there are genes in common using learned operator or the intersect() function.
  1. Create a function to check if the average expression of each sample group is normally distributed (?shapiro.test()) using significance level at 5%. If TRUE, draw directly a histogram (?hist()) for the values. Otherwise, draw a histogram for the log-transformed values. And return the p-value of normality test at the end.

Test your function on average expression of RRP6 samples.

  1. Click “Render” to generate your Quarto report.

The homework correction is available here: link