Genetic data analysis/exploration using R, 16th – 20th August, Millport Field Station, Ilse of Cumbrae, Scotland, delivered by Dr. Thibaut Jombart.
This course will provide an extensive overview of exploratory methods for the analysis of genetic data using the R software and aim to equip participants with powerful resources for tackling increasingly common challenges in genetic data analysis.
The course is aimed at PhD students, research postgraduates, and practicing academics as well as persons in industry and is therefore suitable for ornithologists working with genetic data in fields such as molecular ecology, evolutionary biology, and phylogenetics.
The course is made up from the following 5 modules
Module 1 Introduction to phylogenetic reconstruction • Lecture 1a: Reconstructing phylogenies from genetic sequence data. Three main approaches covered: distance-based phylogenies; maximum parsimony; and likelihood-based approaches. • Lecture 1b: Short R refresher. • Practical 1: Phylogenetic reconstruction using R. Three main approaches plus rooting a tree; assessing/testing for a molecular clock; and bootstrapping. Main packages: ape, phangorn.
Module 2 Introduction to multivariate analysis of genetic data • Lecture 2: Key concepts in multivariate analysis. Focus on using factorial methods for genetic data analysis. • Practical 2: Basics of multivariate analysis of genetic data in R. Topics include: data handling, population genetic tests of population structure (PCA, PCoA). Main packages: adegenet, ade4, ape.
Module 3 Exploring group diversity • Lecture 3: Approaches to identifying and describing genetic clusters. Topics include: hierarchical clustering, K-means, population-level multivariate analysis (between-group-PCA, DA, DAPC). • Practical 3: Applying the approaches covered in morning lecture and emphasising their strengths and weaknesses. Main packages: adegenet, ade4.
Module 4 Spatial genetic structure • Lecture 4: Discussing the origin and significance of spatial genetic patterns, and how to test or them. • Practical 4: Visualising and analysing spatial genetic data. Topics: spatial density estimates, Moran/Mantel tests, mapping principal components in PCA, spatial PCA. • Main packages: adegenet, glmnet. Main packages: adegenet, glmnet.
Module 5 Using R for reproducible science • Lecture 5: Using R for reproducible science. • Practical 5: Practical session based on morning lecture • Main packages: knitr, Sweave, rmarkdown • Option to discuss own data (time permitting)
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Additional related up-coming courses - INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING - LANDSCAPE (POPULATION) GENETIC DATA ANALYSIS USING R - APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS - PHYLOGENETIC DATA ANALYSIS USING R - SPATIAL ANALYSIS OF ECOLOGIC AL DATA USING R - ADVANCING IN STATISTICAL MODELLING USING R - MODEL BASED MULTIVARIATE ANALYSIS OF ECOLOGICAL DATA USING R - NETWORK ANAYLSIS FOR ECOLOGISTS USING R - STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR USING R