Summer Institute in Statistical Genetics
Seattle, July 2019
Statistical Genetics, July 17-19


Course notes

Population genetics data analysis notes


Practicals

    Pre module: R refresher [pdf] [Rmd]
    Wednesday 17th, pm [1kg sample description] [gds file of 10k snps, African samples only] [R code to create this file]

Thursday 18th

Allele frequencies and HW testing

R Markdown version

First analysis of African chr 22 data set

R Markdown version

Friday 19th

Population structure

R Markdown version

Population specific betas and individual coancestries

R markdown version

You need to download the following three files to be able to compile the rmd file:

Rdata set for hapmap

Rdata set for fig 3

Rdata set for pedigree

Individual inbreeding and relatedness

Individual inbreeding, relatedness and k coeffs

R markdown version

Individual PCA and PCOA

1k genome analysis of subset of chr 22

chr22 first 20k snps gds file


Datasets

FBI data set

Hapmap chromosome 2 data

Hapmap Chromosome 2 SNP positions

AMD data set


PDFs

Essentials

Holsinger and Weir 2009, Nature Review Genetics

Weir and Goudet, Genetics 2017

Goudet, Kay and Weir, Molecular Ecology, In revision

Hierfstat related

Hierfstat presentation (Goudet 2005)

Hierfstat tutorial (Demeeus and Goudet 2007)

Import data in Hierfstat (Vignette )

New features in hierfstat (Vignette)

Hierfstat practical

Data set analyses and other stuff

Trouve et al 2004- Galba truncatula hierarchical analysis

Weir and Hill 2002- FBI data set analysis

Weir et al 2005- hapmap data set analysis

Buckleton etal. 2016, Forensic Science International

AMD - amd data set analysis

Graffelman Moreno mid p-value

Balloux et al (2000) microsatellites can be misleading

Brandt et al (2018) FST at MHC in 1000 genomes


Programs

To install a package from CRAN, just type install.packages("pkg.name") where pkg.name is the name of the package to install.

To install Bioconductor, type the following code:

source("https://bioconductor.org/biocLite.R")

biocLite()

To install the SNPRelate package:

biocLite("SNPRelate")

To install the 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)

To install ms, Hudson coalescent simulator, go to:

ms download website

Executable for windows

Executable for linux

Quantinemo tutorials

Tutorials

Review of available population genetics analyses programs

Excoffier and Heckel review

MER special issue Pop genomic resources in R

Bioconductor web site

CRAN taskview on statistical genetics

Available population genetics simulation programs

web site listing