Nov 8-9, 2023
9:00 am - 4:00 pm EDT
Instructors: Sue McClatchy, Dan Gatti, Brian Yandell
Helpers:
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This course introduces genetic mapping using qtl2, a R package for analyzing quantitative phenotypes and genetic data from complex crosses like the Diversity Outbred (DO). Genetic mapping with qtl2 allows researchers in fields as diverse as medicine, evolution, and agriculture to identify specific chromosomal regions that contribute to variation in phenotypes (quantitative trait loci or QTL). The goal is to identify the action, interaction, number, and precise location of these regions. The course concludes with a complete analytical workflow from a study of DO mice. The lesson is adapted from Karl Broman's software, tutorials, and book co-authored with Saunak Sen, A Guide to QTL Mapping with R/qtl.
Who: The course is aimed at researchers who want to employ genetic mapping to identify, quantify, and characterize quantitative trait loci. Prerequisites: Some R programming skills are required for successful participation. If you can manipulate R data structures (e.g. lists, matrices, data frames) you are ready for this course. Knowledge of genetics and statistics will also help you gain the most from this course. To ensure that all participants receive the support that they need during training, remote participation will not be made available. You must attend in person and on-site.
Where: 600 Main Street, Bar Harbor ME. Get directions with OpenStreetMap or Google Maps.
When: Nov 8-9, 2023. Add to your Google Calendar.
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.). They should have a few specific software packages installed (listed below).
Accessibility: We are committed to making this workshop accessible to everybody. For workshops at a physical location, the workshop organizers have checked that:
Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.
Contact: Please email susan.mcclatchy@jax.org for more information.
Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
| Before | Follow setup instructions |
| 09:00 | Introductions and Workshop Overview |
| 09:30 | Quantitative trait locus mapping in multiparent crosses (download ppt) |
| 10:45 | Coffee |
| 11:00 | Input File Format |
| 11:30 | Calculating Genotype Probabilities |
| 12:30 | Lunch |
| 1:30 | Special covariates for the X chromosome |
| 2:00 | Performing a genome scan |
| 2:45 | Coffee |
| 3:00 | Performing a permutation test |
| 3:30 | Finding LOD peaks |
| 3:55 | Wrap-up |
| 4:00 | End |
| 09:00 | A Bird's Eye View of QTLs |
| 09:30 | Recap: genome scans and permutation tests |
| 09:45 | Finding LOD peaks (continued) |
| 10:15 | Calculating A Kinship Matrix |
| 10:45 | Coffee |
| 11:00 | Calculating A Kinship Matrix (continued) |
| 11:30 | Performing a genome scan with a linear mixed model |
| 12:30 | Lunch |
| 1:30 | Estimated QTL effects |
| 2:00 | QTL analysis in Diversity Outbred Mice |
| 2:45 | Coffee |
| 3:00 | QTL analysis in Diversity Outbred Mice (continued) |
| 3:55 | Wrap-up |
| 4:00 | End |
To participate in a workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.
We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.
R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.
Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.
Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.
Instructions for R installation on various Linux platforms (debian,
fedora, redhat, and ubuntu) can be found at
<https://cran.r-project.org/bin/linux/>. These will instruct you to
use your package manager (e.g. for Fedora run
sudo dnf install R and for Debian/Ubuntu, add a ppa
repository and then run sudo apt-get install r-base).
Also, please install the
RStudio IDE.
The qtl2 package contains code for haplotype reconstruction, QTL mapping and plotting.
Install R/qtl2 from https://cran.r-project.org/:
install.packages("qtl2")
Make a new folder in your Desktop called mapping. Move into this new folder.
Create a data folder to hold the data, a scripts folder to house your scripts, and
a results folder to hold results.
Alternatively, you can use the R console to run the following commands for steps 1 and 2.
setwd("~/Desktop")
dir.create("./mapping")
setwd("~/Desktop/mapping")
dir.create("./data")
dir.create("./scripts")
dir.create("./results")
data folder. You can download the files from the URLs below and move the files the
same way that you would for downloading and moving any other kind of data.Alternatively, you can copy and paste the following into the R console to download the data.
setwd("~/Desktop/mapping")
download.file("https://ndownloader.figshare.com/files/9746485", "./data/cc_variants.sqlite")
download.file("https://ndownloader.figshare.com/files/9746458", "./data/mouse_genes.sqlite")
download.file("https://ndownloader.figshare.com/files/9746452", "./data/mouse_genes_mgi.sqlite")
Mac and Linux machines can load the DO demonstration data with this code.
download.file(url="ftp://ftp.jax.org/dgatti/qtl2_workshop/qtl2_demo.Rdata", destfile="./data/qtl2_demo.Rdata")
Windows machines must add the argument mode=wb to the download.file() command
download.file(url="ftp://ftp.jax.org/dgatti/qtl2_workshop/qtl2_demo.Rdata", destfile="./data/qtl2_demo.Rdata", mode = "wb")
You will need these for the final lesson episodes on SNP association mapping and QTL analysis in Diversity Outbred mice.