Instructor Notes
This is a placeholder file. Please add content here.
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
Performing a permutation test
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
Replace number of permutations (1000) with 100 for expediency. 1000 permutations takes 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
Integrating Gene Expression Data
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.