ONLINE COURSE – Fundamentals of populations genetics using R (FOPG01) This course will be delivered live
14 September 2020 - 18 September 2020£500.00
This course will now be delivered live by video link in light of travel restrictions due to the COVID-19 (Coronavirus) outbreak.
This is a ‘LIVE COURSE’ – the instructor will be delivering lectures and coaching attendees through the accompanying computer practical’s via video link, a good internet connection is essential.
TIME ZONE – Western European Summer Time – however all sessions will be recorded and made available allowing attendees from different time zones to follow a day behind with an additional 1/2 days support after the official course finish date (please email firstname.lastname@example.org for full details or to discuss how we can accommodate you).
The aim of the course is to introduce you to the fundamentals of population genetics theory, through quantitative visualizations of the dynamic of genetic elements within and between populations, using the R statistical programming language. We will be using a mixture of lectures, exercises, and case studies to increase the intuitive understanding of population genetics concepts and facilitate conceptual experimentation and visualization in R.
By the end of the course participants should:
1. Understand the fundamentals of population genetics theory
2. Be able to use R to visualize data sets and write simple functions
3. Know how to import different data types into and out of R
4. Create simple population genetics simulations in R
5. Understand essential summary statistics from the population genetics literature (e.g. FST , D, pi, theta, etc.)
6. Be able to generate publication quality figures from population genetic data
TAcademics and students working on projects related to population genetics that want to a gain a better conceptual grasp of theory and the statistics tool R.
The course is designed for R beginners who have prior exposure to population genetics concepts and intermediate-to-advanced R users interested in learning population genetics theory.
Venue – Delivered remotely
Time zone -Eastern Daylight time
Availability – 30 places
Duration – 4.5 days
Contact hours – Approx. 30 hours
ECT’s – Equal to 3ECT’s
Language – English
PLEASE READ – CANCELLATION POLICY: Cancellations are accepted up to 28 days before the course start date subject to a 25% cancellation fee. Cancellations later than this may be considered, contact email@example.com. Failure to attend will result in the full cost of the course being charged. In the unfortunate event that a course is cancelled due to unforeseen circumstances a full refund of the course fees will be credited.
The course will be a mixture of theoretical and practical. Each concept will be first described and explained, and next there will be a time to exercise the topics using provided data sets. Participants are also very welcome to bring their own data.
Assumed quantitative knowledge
The course is designed for intermediate-to-advanced R users interested in population genetics and R beginners who have prior experience with some population genetics concepts.
Assumed computer background
We assume a very fundamental prior experience with the R language, or programming generally. However, if you do not have any R or programming experience but are familiar with basic population genetics concepts such as allele vs genotype frequencies, or FST calculations, this course may still be useful to you.
Equipment and software requirements
A laptop/personal computer with a working version or R and RStudio installed. R and RStudio are supported by both PC and MAC and can be downloaded for free by following these links
UNSURE ABOUT SUITABLILITY THEN PLEASE ASK firstname.lastname@example.org
Monday 14th – Classes from 09:30 to 17:30
1) Introduction to the course
2) Learning through programming
3) Key concepts related to population genetic data
4) Generating and switching between R data classes
5) Reading different types of genetic data into R
6) Understanding R’s statistical toolbox
Tuesday 15th – Classes from 09:30 to 17:30
1) Introduction to the Hardy-Weinberg equilibrium assumption
2) Allele frequencies vs genotype frequencies
3) Probability and likelihood in pop. gen.
4) Generating basic simulations in R
5) Introduction to algorithms
6) Expectation-maximization of likelihood
Wednesday 16th – Classes from 09:30 to 17:30
1) Interpreting violations of expectations
2) More complex genetic data (multiple loci)
3) Fitness and selection on genetic elements
4) Neutral variation and genetic drift
5) Population assignment and comparison
6) 2D and 3D visualization in R
Thursday 17th – Classes from 09:30 to 17:30
1) Disentangling neutral and non-neutral processes
2) Implementing coalescent theory
3) Retrieving open data from web sources
4) Using R packages for data retrieval
5) Reading and writing data files in R
Friday 18th – Classes from TBC
1) 1/2 Day for catch up sessions to cater for different time zones to
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