BMI 826-001: Statistical methods for QTL mapping (Fall, 2012)

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Schedule

[Note: the following is subject to revision.]

Date Topic   Reading Homework
Sep4 (1) Overview Ch 1
6 (2) Meiosis and recombination
 
11 (3) Hidden Markov models (HMMs) for QTL mapping App D
13 (4) Data diagnostics Ch 3 | example (protected)
 
18 (5) Genetic map construction tech report HW 1 (due 10/2)
[Data: hw1.csv]
20 (6) Interval mapping Sec 4.1-4.2
 
25 (7) Selective genotyping; significance thresholds;
interval estimates of QTL location; selection bias
Sec 4.3, 4.5
27 (8) Non-normal traits Ch 5
 
Oct2 (9) Experimental design and power Ch 6 | code HW 2 (due 10/18)
[Data: hw2.csv]
4 No lecture
 
9 (10) Covariates Ch 7 | R code
11 (11) Two-dimensional, two-QTL genome scans Ch 8 | slides (pdf) | R code | hyper_demo_stuff.RData
 
16 (12) The X chromosome Sec 4.4 | code
18 (13) Mapping multiple QTL I Sec 7.4; Ch 9 HW 3 (due 11/8)
[Data: hw3.csv]
 
23 (14) Mapping multiple QTL II slides (pdf)
25 (15) Multiple QTL mapping in R/qtl R code | .RData file HW 4 (due 11/15-ish)
[hw4_data.csv | paper |
hw4_data.RData | hw4_perms.RData]
 
30 No lecture
Nov1 No lecture
 
6 (16) Bayesian methods
8 (17) RIL and AIL
 
13 (18) eQTL analysis review article
15 (19) Detecting sample mix-ups in eQTL data slides (pdf) | R/lineup package


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Last modified: Tue Nov 20 12:51:35 2012