I am taking the opportunity to sit in Ruth Shaw's quantitative genetics class this semester.  I hope that I get to teach this class at some point in the future and I thought it would be great to see how a pro like Ruth teaches this class.  Listening to her lecture and show slides today though inspired me to make a little app that I would like my future students to have.  We are using Falconer and Mackay and in chapter 6 they are attempting to explain the effect of the number of loci on the expected distribution of observed phenotypes.  The students were shown this graph



Students made the connection to why you would get a good approximation of a normal distribution when you have a large number of loci.    However, I thought though that it would be pretty easy to make a web page with the R package Shiny that would recapitulate this graph and let your students see how things change as a function of the different parameters involved.  The solution that I wrote up includes parameters for:

a: genotypic value - this is just the phenotypic measure of the homozygous A2A2 in contrast, the A1A1 homozygote will have a phenotypic measure of -a.

d: degree of dominance- the measure of how the heterozygous individual deviates from the expected value of 0 (a-a).

mean p: mean allele frequency- unlike in the example I want to allow allele frequency at each locus to be a random draw from a truncated normal distribution with a minimum value of 0 and a maximum value of 1.

var p: variance in allele frequency- just describes the distribution that we are drawing allele frequencies from.

loci: the number of loci affecting the trait of interest.

samp: sample size- rather than calculating the probabilities I want to take samples from a population to reinforce the importance and impact of sample size on our ability to understand a system.

Finally, I have a resample button that lets us go take another sample from the population.


Here is a link to the web app: https://popgensim.shinyapps.io/loci_num/


I should probably get back to writing papers and applying for faculty positions!

cheers