Computational biology and genomics
Last updated: 2023/10/11 A key measure in information theory is entropy, which is: "The amount of uncertainty involved in a random process; the lower the uncertainty, the lower the entropy." For example, there is lower entropy in a fair coin flip versus a fair die roll since there are more possible outcomes with a die…
Updated 10th September 2013 to include LAST I previously looked at mapping repeats with respect to sequencing errors in high throughput sequencing and as one would expect, the accuracy of the mapping decreased when sequencing errors were introduced. I then looked at aligning to unique regions of the genome to get an idea of how…
This deserved its own post because I had some difficulty understanding the double square brackets in R. If we search for “double square brackets in R” we come across this tutorial, which shows us that the double square brackets, i.e. [[]], can be used to directly access columns:
Here I demonstrate the distance matrix computations using the R function dist(). Firstly let’s prepare a small dataset to work with: How does this dataset look in 3 dimensional space? We can see that points 4 and 6 are quite far away from each other.
I’ve just started the Mathematical Biostatistics Boot Camp 1 and to help me remember the set notations introduced in the first lecture, I’ll include them here: The sample space, $$\Omega$$ (upper case omega), is the collection of possible outcomes of an experiment, such as a die roll: $$!\Omega = \{1, 2, 3, 4, 5, 6\}$$…