Special Topics in Genetics and Genomics (140.668)


Second Term, 2006-2007

Instructor:  Karl Broman
Office hours: F 10:30-12:00 in E3612 Wolfe St
Topic: Mapping quantitative trait loci in experimental crosses
Prerequisites: 140.651-654; knowledge of the computer package R.
Course time: Monday and Wednesday, 10:30 - 11:50am
Course room: W4007 SPH
Software: R and R/qtl
Grades: Class discussion and a final project.
Final project: Visit the QTL archive, and register and select a data set.

Analyze the data, and write a short (5-10 pages) paper describing the data, your analysis methods, and your results. If possible, compare your results to the other publications on the chosen data.


Syllabus

Date Topic
Oct30 Overview of QTL mapping
Nov1 Meiosis, recombination, and crossover interference
6 Discussion of readings
8 Hidden Markov models
13 Discussion of readings
15 Standard interval mapping
20 Discussion of readings
22 Interval mapping variants
27 Discussion of readings
29 Interval mapping with other phenotype models
Dec4 Discussion of readings
Sample R/qtl code: [
prepData.R | analysis.R]
6 Covariates, composite interval mapping
11 Discussion of readings
13 2d scans, multiple QTL analysis
18 Discussion of readings
20 More modern things


Course home page

Last modified: Wed Apr 15 23:09:22 2009