Instructor Notes

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Introduction to the Data Set

Input File Format

Calculating Genotype Probabilities

Instructor Note

We need the following block for the site to build on Github. The students do not need to see or run the next block.


Performing a Genome Scan

Calculating A Kinship Matrix

Performing a genome scan with a linear mixed model

Performing a Genome Scan with Binary Traits

Finding Significant Peaks via Permutation

Instructor Note

We need the following block for the site to build on Github. The students do not need to see or run the next block.


Instructor Note

Permutations are computationally intensive and might take a long time on some machines. Start with n_perm=10 and ask participants to place a sticky note on their laptop screen once this has finished. Repeat with n_perm=100 for those whose permutations completed in a reasonable amount of time (a minute or less). Try n_perm=1000 if all went well previously. 1000 permutations should take about 2 minutes.


Finding QTL peaks

Instructor Note

We need the following block for the site to build on Github. The students do not need to see or run the next block.


Estimating QTL effects

Instructor Note

Don’t have the students type all of this. Copy and paste or show this code in a web browser.


Integrating Gene Expression Data

Instructor Note

This may be a good code chunk to have the students copy and paste.


QTL Mapping in Diversity Outbred Mice

Instructor Note

The code below is needed to load in the data objects to build the lesson on Github. The *.Rdata file is over 200 Mb and Github has a file size limit of 100 Mb. The students should NOT run the next block.


Instructor Note

This is the only block that the students need to run.


Instructor Note

Remember, you just need to show the basic plot. Just type out the ggplot, geom, log scale, and facet wrap lines in class.


Instructor Note

This code is intended to throw an error. It is used to illustrate the point that you have to align the markers between probs and map.


Instructor Note

Note that you have to add the genes, colors, and top_panel_prop arguments.


Instructor Note

Note that you have to change the top_panel_prop argument to panel_prop and add the drop_hilit, col_hilit, and sdp_panel arguments.