SISG Seattle 2015
module Population genetic data analysis, July 13th-15th

Course notes

R refresher

R tutorial

R markdown version

Practicals

Monday 13th, AM

Monday 13th PM

Allele frequencies and HW testing

R Markdown version

Tuesday 14th AM

EM exercice recessive allele

R Markdown version

Tuesday 14th PM

Population structure

R Markdown version

Population specific betas

R Markdown version

To install latest version of hierfstat (on github), do the following:

Install devtools using install.packages("devtools")

load it in R using library(devtools)

Install hierfstat from github using install_github("jgx65/hierfstat")

load it in R using library(hierfstat)

check that it is the latest version (0.04-15) by typing example(betas)

Wednesday 15th AM

Ratio of homozygosity when inbred

R markdown version

Individual inbreeding and relatedness, and GWAS

R markdown version

Datasets

FBI data set

Hapmap chromosome 2 data

Hapmap Chromosome 2 SNP positions

AMD data set

PDFs

Holsinger and Weir 2009, Nature Review Genetics

Hierfstat presentation (Goudet 2005)

Hierfstat tutorial (Demeeus and Goudet 2007)

Weir and Hill 2002- FBI data set analysis

Trouve et al 2004- Galba truncatula hierarchical analysis

Weir et al 2005- hapmap data set analysis

AMD - amd data set analysis

Graffelman Moreno mid p-value

Balloux et al (2000) microsatellites can be misleading