In magnusdv/pedsuite: Easy Installation of the 'pedsuite' Packages for Pedigree Analysis

knitr::opts_chunk$set(echo = TRUE, 
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• Dates: October 7, 14, 21 and 28, 2024
• Where: Online, as part of GHEP-ISFG Online School 2024
• Teachers: Magnus D. Vigeland and Thore Egeland
• Audience: Students, researchers and case workers in forensic genetics

Learning outcomes

• Classical concepts and methods of genetic relatedness
• Using QuickPed and other apps for pedigree analysis
• Using Familias software to perform kinship testing
• Methods for relationship inference and pedigree reconstruction
• Practical methods for disaster victim identification

Software preparation: R

Several exercises will use R. In order to do them, please install the following on your computer:

• A recent version of R
• RStudio

Run the following command in R to install the pedsuite packages:

install.packages("pedsuite")

Software preparation: Familias

Part of the course is based on kinship testing in the Familias software, which can be installed here: https://familias.no/download.

Schedule

The course runs each Monday of October 2024, from 16 to 20 (CEST). The following schedule is tentative:

link = pedsuite:::linkFUN(folder = "courses/ghep2024")

Oct 7: Theory of relatedness

• 16:00--17:00 r link("Introduction to pedigrees, QuickPed and R", "ghep2024_lecture1_pedigrees.pdf") (MDV)
• 17:00--17:45 r link("Exercises I", "exercises1.pdf")
• 17:45--18:00 Break
• 18:00--19:00 r link("Measures of relatedness", "ghep2024_lecture2_coefficients.pdf") (MDV)
• 19:00--19:45 r link("Exercises II", "exercises2.pdf")
• 19:45--20:00 Wrap-up

Oct 14: Kinship testing

• 16:00--17:00 r link("Introduction to forensic kinship testing", "ghep2024_lecture3_testing.pdf") (TE)
• 17:00--17:45 r link("Exercises III", "exercises3.pdf")
• 17:45--18:00 Break
• 18:00--19:00 r link("Kinship testing with Familias", "ghep2024_lecture4_Familias.pdf") (TE)
• 19:00--19:45 r link("Exercises IV", "exercises4.pdf"). File needed: r link("kinship-riddle.fam")
• 19:45--20:00 Wrap-up

Oct 21: Relatedness inference

• 16:00--17:00 r link("Realised relatedness: Why are some siblings more alike than others?", "ghep2024_lecture5_realised.pdf") (MDV)
• 17:00--17:45 r link("Exercises V", "exercises5.pdf")
• 17:45--18:00 Break
• 18:00--19:00 r link("Pedigree reconstruction", "ghep2024_lecture6_reconstruction.pdf") (MDV)
• 19:00--19:45 r link("Exercises VI", "exercises6.pdf")
• 19:45--20:00 Wrap-up

Oct 28: Disaster victim identification

• 16:00--17:00 r link("DNA-based disaster victim identification", "ghep2024_lecture7_DVI_Familias.pdf") (TE)
• 17:00--17:45 r link("Exercises VII", "exercises7.pdf"). Familias file: r link("planecrash.fam")
• 17:45--18:00 Break
• 18:00--19:00 r link("Practical DVI with Diviana", "ghep2024_lecture8_diviana.pdf") (MDV)
• 19:00--19:45 r link("Exercises VIII", "exercises8.pdf")
• 19:45--20:00 Wrap-up

Solutions to the exercises can be requested by email to magnusdv at gmail dot com.

magnusdv/pedsuite documentation built on Nov. 4, 2024, 9:36 p.m.