SISG, in person -- July 17-19, 2023
Module: Statistical Genetics

Instructors:

Bruce Weir: [web]
Jerome Goudet: [web]

Schedule

Pre module

List of programs to install before the module (see programs for details)

Before everything else, make sure that the programs and packages below are installed before the class. In order to install these, you very likely need to have admin access to your hard disk and system. If you do not have these accesses, ask your local IT person to install them, again, before the class.

R related


• must install: R [web]
• must install: R studio [web]
  
• To install a package from CRAN, just type
  install.packages("pkg.name")
  from the R prompt, where pkg.name is the name of the package to install
• To install packages from github, you'll need the devtools package:
  install.packages("devtools")
  and load it with
  library(devtools)
  then install the package with
  install_github("pkg.name")
• To install packages from Bioconductor, issue the following:
  if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager"); BiocManager::install()

List of R packages to install:

must:

• gaston, hierfstat, HardyWeinberg, adegenet: install.packages(c("gaston","hierfstat","HardyWeinberg","adegenet"))
• from github: JGTeach: install_github("jgx65/JGTeach")


Good to install:
• R packages: pegas, ape: install.packages(c("pegas","ape"))
• Bioconductor: SNPRelate,gdsfmt,SeqArray,SeqVarTools: BiocManager::install(c("SNPRelate","gdsfmt","SeqArray","SeqVarTools"))

Non R
Good to install:


• Hudson' ms: [web]; [exe] (windows) ; [exe] (linux)
• plink 2.0: [web]
• QuantiNemo: [web]



• Finally, download the Datasets over a good internet connection and make sure you remember where they are located on your computer

Course notes

1. Allele frequencies and Variances
2. Hardy Weinberg Equilibrium
3. Inbreeding and Relatedness
4. Population Structure
5. Quantitative Trait Analyses. Heritability and GWAS

Practicals

1. Practical 1: Loading genetic data into R, Simulating Data, Allelic frequencies [html]
2. Practical 2: Hardy Weinberg equilibrium[html]
3. Practical 3: Inbreeding and kinship[html]
4. Practical 4: population structure[html]
5. Practical 5: Quantitative genetics and heritability estimation[html]

Datasets

• 1000 genomes chromosome 22:
  Large files, download only over a good internet connection
  [VCF]; [gds]; [bed]; [fam]; [bim]
  
• 1000 genomes chromosome 22 first 20 megabases: [VCF]; [gds]
• Matching for 1000 genomes samples based on chr22:0-20M [RDS]
• Cross product of centered, scaled dosage (X matrix) for 1000 genomes samples based on chr22:0-20M at MAF 0.05 [RDS]
• Simulated panmictic population [txt]
• Simulated 3 pops drifting 50 gen [txt]
• Monogamous pedigree [txt]
• Monogamous genotypes from individuals from pedigree [RDS]
• Simulated 4 islands [txt]

PDFs

Essentials

• Holsinger and Weir 2009, Nature Review Genetics: [pdf]
• Speed and Balding 2015 (NRG): [web]
• Weir and Goudet, Genetics 2017:[web]
• Goudet, Kay and Weir, Molecular Ecology, 2018: [web]
• Zhang, Goudet and Weir, Heredity, 2022: [pdf]
• Graffelman and Moreno mid p-value[pdf]

PCA in pop genomics


• Abegaz et al., briefings in bioinformatics 2019[web]
• Patterson etal, Population Structure and Eigenanalysis 2006: [web]
• Novembre and Stephens, Interpreting PCA of spatial population genetic variation, 2008: [web]

Mixed models


• Dandine-Roulland & Perdry, human heredity 2015 [web]

Hierfstat related

• Hierfstat presentation (Goudet 2005): [pdf]
• Hierfstat tutorial (Demeeus and Goudet 2007): [pdf]

Data set analyses and other stuff

• Trouve et al 2004- Galba truncatula hierarchical analysis: [pdf]
• Weir and Hill 2002- FBI data set analysis: [pdf]
• Weir et al 2005- hapmap data set analysis: [pdf]
• Buckleton etal. 2016, Forensic Science International: [pdf]
• AMD - amd data set analysis: [pdf]
• Balloux et al (2000) microsatellites can be misleading: [pdf]
• Brandt et al (2018) FST at MHC in 1000 genomes: [pdf]
• Marostica et al. (2022) HLA diversity apportionment in humans [html]

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 a package from github, you need to install the devtools package first
  install.packages("devtools")
  then load it
  library(devtools)
  and finally install the package using
  install_github("pkg.name")
• To install Bioconductor, type the following code:
  if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install()
• Installing the SNPRelate package, from R prompt:
  BiocManager::install("SNPRelate")

ms and msprime (mspms)

• Hudson's ms, coalescent simulator [web] ; [exe] (win); [exe] (linux)
• Kelleher's msprime: [web]. Trickier to install, but way faster. mspms (part of msprime) has the same syntax as ms
• Messer's SLIM [web] efficient forward in time simulator, becoming the standard for simulations involving selection

QuantiNemo: [web]

Review of available population genetics analyses programs

• Excoffier and Heckel review: [pdf]
• MER special issue Pop genomic resources in R: [web]
• Bioconductor web site: [web]
• CRAN taskview on statistical genetics: No longer available, check [web] for possible updates
• Available population genetics simulation programs: [web]