2022 Genomics & Big Data - R practical exam

Please read the following:

• This is an open book exam. You are allowed to use the practical material, your own answers and Google.
• NOTE: if you use or adapt code that you found with Google, include the link(s) to the page(s) that you used.
• This is an individual exam. You are not allowed to collaborate with others.
• Please hand in an R script, named s123456.R where s123456 is your student number, with the questions clearly marked with comments (using the # character). Please don’t include any unnecessary code, only the code that is used to produce the answer.
• Use R to get the full answer. For instance, if you need to get the highest value of a certain property, use R to get that specific value, don’t just print a sorted dataframe or tibble.

Question 1

The palmerpenguins data contains size measurements for three penguin species observed on three islands in the Palmer Archipelago, Antarctica. The data is available as an R package, but for this exam, you can load the following CSV file:

https://mbdata.science.ru.nl/share/heeringen/R_exam_gbd/penguins.csv

1. How many observations does this data set contain?

2. What is the most commonly observed penguin species in this data set?

3. For how many observations is the sex not recorded?

4. Is there a significant correlation between flipper length and bill depth for the penguin species Chinstrap?

5. Plot the mean bill length against the mean bill depth. Color by species. Note: this plot should contain 3 points.

6. Plot the mean body mass observed over the years. Facet by species and color by sex.

7. We have the hypothesis that male Chinstrap penguins will have a higher body mass than female Chinstrap penguins. Use everything that you have learned to test this hypothesis. What is your conclusion?

Question 2

In June 2021, Hotaling et al. published an inventory of insect genome assemblies. The accompanying data contains information such as assembly size, contig N50 and the type of sequencing technology that was used.

You can load this data set from the following CSV file:

https://mbdata.science.ru.nl/share/heeringen/R_exam_gbd/insects.csv

The contig N50 is a measure of genome quality. It is definied as the sequence length of the shortest contig at 50% of the total genome length.

The column BUSCO_complete contains information on gene annotation quality. The BUSCO gene set contains genes that should be conserved in all insects. The BUSCO_complete column defines how many of these genes are present in the given assembly.

1. Which order has the largest mean genome size?

2. The following is a figure from the paper. Re-create this figure as best as you can. Note: you don’t have to re-create the specific grouping of the X-axis, you can group by order. In addition, you do not have to create the grey background shading.